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A field experiment was conducted to assess the impact of various planting densities and levels of shoot thinning on cut flower yield, quality, soil chemical properties and cost economics in the commercially cultivated alstroemeria cultivar 'Capri'. The experiment involved three planting densities (4, 6 and 8 plants/m2) along with three shoot thinning levels (10 %, 20 % and 30 %). It was observed that higher planting density (4 plants/m2) promoted the length of cut stem, early bud formation, and flowering, optimal quality parameters, including maximum stem thickness, cut stem weight, floret quantity/stem, floret size, number of flowering stems/plant (yield) and vase life. Exclusive use of higher vegetative mass removal (30 % shoot thinning) was found to improve quality parameters such as the length of cut stem, number of flowering stems, stem thickness, weight of cut stem, floret quantity/stem, floret size, vase life, and early flowering. Soil samples were collected from each treatment and the consequent lab analysis revealed that the lower planting density and shoot thinning level resulted in maximum soil organic carbon, nitrogen, phosphorous and potassium content. In conclusion, planting density of 4 plants/m2 and 30 % shoot thinning emerged as the optimal combination for enhancing quantitative parameters in commercial alstroemeria cultivation. The study underscores the importance of strategic planting practices and vegetative mass management for maximizing yield and quality in alstroemeria production, along with ensuring higher economic returns.

Comparing accuracies of structural protein–protein interaction (PPI) models for different complexes on an absolute scale is a challenge, requiring normalization of scores across structures of different sizes and shapes. To help address this challenge, we have developed a statistical significance metric for docking models, called random‐docking (RD) p‐value. This score evaluates a PPI model based on how likely a random docking process is to produce a model of better or equal accuracy. The binding partners are randomly docked against each other a large number of times, and the probability of sampling a model of equal or greater accuracy from this reference distribution is the RD p‐value. Using a subset of top predicted models from CAPRI (Critical Assessment of PRediction of Interactions) rounds over 2017–2020, we find that the ease of achieving a given root mean squared deviation or DOCKQ score varies considerably by target; achieving the same relative metric can be thousands of times easier for one complex compared to another. In contrast, RD p‐values inherently normalize scores for models of different complexes, making them globally comparable. Furthermore, one can calculate RD p‐values after generating a reference distribution that accounts for prior information about the interface geometry, such as residues involved in binding, by giving the random‐docking process access the same information. Thus, one can decouple improvements in prediction accuracy that arise solely from basic modeling constraints from those due to the rest of the method. We provide efficient code for computing RD p‐values at https://github.com/Grigoryanlab/RDP. [ABSTRACT FROM AUTHOR]

We present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody–antigen complexes, and 7 large assemblies. On average ~70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups and by 15 CAPRI scorer groups were evaluated using the CAPRI model quality measures and the DockQ score consolidating these measures. The prediction performance was quantified by a weighted score based on the number of models of acceptable quality or higher submitted by each group among their five best models. Results show substantial progress achieved across a significant fraction of the 60+ participating groups. High-quality models were produced for about 40% of the targets compared to 8% two years earlier. This remarkable improvement is due to the wide use of the AlphaFold2 and AlphaFold2-Multimer software and the confidence metrics they provide. Notably, expanded sampling of candidate solutions by manipulating these deep learning inference engines, enriching multiple sequence alignments, or integration of advanced modeling tools, enabled top performing groups to exceed the performance of a standard AlphaFold2-Multimer version used as a yard stick. This notwithstanding, performance remained poor for complexes with antibodies and nanobodies, where evolutionary relationships between the binding partners are lacking, and for complexes featuring conformational flexibility, clearly indicating that the prediction of protein complexes remains a challenging problem. [ABSTRACT FROM AUTHOR]

This paper presents an analysis of the potential socio-economic implications of the European Commission's policy initiative to ban the use of cages in EU livestock farming, with a specific focus on conventional farrowing crates in the pig sector. Using the CAPRI (Common Agricultural Policy Regionalised Impact) tool, a multi-purpose comparative-static partial equilibrium modelling framework, the study examines two scenarios: an immediate phase-out of conventional farrowing crates by 2025 and a 10-year transition period until 2035. The simulation results indicate that the ban would lead to a significant decline in pork production in the EU, with production decreasing by 23.6% in the immediate phase-out scenario and by 8.4% in the 10-year transition scenario. The decline in production affects domestic demand and weakens the EU's net trade position. However, the ban would also result in an increase in consumer prices and producer prices for pork, partly moderating the decline in profits for the pig sector. Moreover, the study highlights the interconnectedness of agricultural policies and the importance of a global assessment of their impact on greenhouse gas (GHG) emissions. The simultaneous decline in EU pork exports and increase in EU pork imports trigger emission leakage: while GHG emissions from EU pork production are significantly reduced, the Global Warming Potential (GWP) of non-EU pork production increases by 4.2%. We find that the length of the transition period fundamentally defines the potential economic effects on the EU pig industry, the impacts on trade balance, and on global environmental effects. This finding emphasises that the implementation details of policy initiatives must be carefully designed to address both domestic and foreign challenges arising from the sustainable transformation of livestock farming practices in the EU. [ABSTRACT FROM AUTHOR]

In some of their works, Maxim Gorky (1868-1936) and Mykhailo Kotsiubynsky (1864-1913) were inspired by their long stay in Capri. At that time, both authors were subjects of the Russian tsar, belonging to the same generation, and later became part of the Russian and Ukrainian literary canon, respectively. It was on the Italian island that they were able to meet and begin a friendship based on great mutual respect. In this article, after recounting the experience the two writers shared on the Italian island, I will analyze and compare excerpts from Gorky's well-known Italian Tales (Skazki ob Italii) and Kotsiubynsky's less famous The Dream (Son) and On the Island (Na ostrovi). More specifically, I would like to demonstrate how Gorky's texts are more characterized by a realistic approach with social elements, while in the texts of Kotsiubynsky the details of the landscape fade into a literary impressionism with fairy-tale traits. However, in both cases the sunny island of Capri symbolizes the beginning of a completely new life (for the lyrical subject or even for the whole of humanity). [ABSTRACT FROM AUTHOR]

In 1858 Józef Ignacy Kraszewski accomplished a trip around Italy, which was described in his travel diary Kartki z podróży 1858-1864 (Travel pages 1858-1864). Kraszewski's aims as an artist and art critic were to deepen his theoretical knowledge, to see the Antique Rome, since he was fascinated by archaeology and history, and visit Dante's city, because he had translated The Divine Comedy around 1864. Thanks to his travels, Italy became a more familiar and sensitive place to read the signs of the past. The ruins of Herculaneum and Pompeii tell the story of an ancient past, not only offering an investigation into the meaning of existence, but also helping to grasp the meaning and direction of modern changes. [ABSTRACT FROM AUTHOR]

The author of the article actualises the Italian genotext of A.M. Gorky's creativity of the Capri period. Neither before nor after the work of "the Stormy Petrel of the Revolution" was characterised by such a joyful and "spiritually uplifting" worldview as it was on the island of Capri. Despite the fact that Gorky wrote about Russian life, his works of this period reveal an "Italian palimpsest", which became the subject of analysis. Gorky's works Confession (1907-1908), Summer (1909), Gorodok Okurov (1909-1910), The Life of Matvei Kozhemyakin (1910-1911) have not been analysed by researchers from the point of view of the Italian presence. The Italian palimpsest of Gorky's Capri oeuvre was first brought to the attention of one of the first chroniclers of "Russian Capri", the writer Alexei Zolotarev, who pointed out the main peculiarity of this period of the writer's work, which still raises many questions for literary historians. [ABSTRACT FROM AUTHOR]

Peptide-protein docking is challenging due to the considerable conformational freedom of the peptide. CAPRI rounds 38-45 included two peptide-protein interactions, both characterized by a peptide forming an additional beta strand of a beta sheet in the receptor. Using the Rosetta FlexPepDock peptide docking protocol we generated top-performing, high-accuracy models for targets 134 and 135, involving an interaction between a peptide derived from L-MAG with DLC8. In addition, we were able to generate the only medium-accuracy models for a particularly challenging target, T121. In contrast to the classical peptide-mediated interaction, in which receptor side chains contact both peptide backbone and side chains, beta-sheet complementation involves a major contribution to binding by hydrogen bonds between main chain atoms. To establish how binding affinity and specificity are established in this special class of peptide-protein interactions, we extracted PeptiDBeta, a benchmark of solved structures of different protein domains that are bound by peptides via beta-sheet complementation, and tested our protocol for global peptide-docking PIPER-FlexPepDock on this dataset. We find that the beta-strand part of the peptide is sufficient to generate approximate and even high resolution models of many interactions, but inclusion of adjacent motif residues often provides additional information necessary to achieve high resolution model quality.

Advances in a scientific discipline are often measured by small, incremental steps. In this review, we report on two intertwined disciplines in the protein structure prediction field, modeling of single chains and modeling of complexes, that have over decades emulated this pattern, as monitored by the community-wide blind prediction experiments CASP and CAPRI. However, over the past few years, dramatic advances were observed for the accurate prediction of single protein chains, driven by a surge of deep learning methodologies entering the prediction field. We review the mainscientific developments that enabled these recent breakthroughs and feature the important role of blind prediction experiments in building up and nurturing the structure prediction field. We discuss how the new wave of artificial intelligence–based methods is impacting the fields of computational and experimental structural biology and highlight areas in which deep learning methods are likely to lead to future developments, provided that major challenges are overcome. [ABSTRACT FROM AUTHOR]

[Display omitted] • CAPRI has catalyzed the development and defines the state of the art in the modeling of protein complexes. • DOCKGROUND is an established and regularly updated resource for protein complexes. • The CAPRI-Q resource applies the CAPRI assessment metrics to any number of submitted model structures and classifies them following CAPRI criteria. • The CAPRI-Q source code is freely available. • The CAPRI-Q web server is fully integrated into the DOCKGROUND resource. Protein interactions are essential for cellular processes. In recent years there has been significant progress in computational prediction of 3D structures of individual protein chains, with the best-performing algorithms reaching sub-Ångström accuracy. These techniques are now finding their way into the prediction of protein interactions, adding to the existing modeling approaches. The community-wide Critical Assessment of Predicted Interactions (CAPRI) has been a catalyst for the development of procedures for the structural modeling of protein assemblies by organizing blind prediction experiments. The predicted structures are assessed against unpublished experimentally determined structures using a set of metrics with proven robustness that have been established in the CAPRI community. In addition, several advanced benchmarking databases provide targets against which users can test docking and assembly modeling software. These include the Protein-Protein Docking Benchmark, the CAPRI Scoreset, and the Dockground database, all developed by members of the CAPRI community. Here we present CAPRI-Q, a stand-alone model quality assessment tool, which can be freely downloaded or used via a publicly available web server. This tool applies the CAPRI metrics to assess the quality of query structures against given target structures, along with other popular quality metrics such as DockQ, TM-score and l -DDT, and classifies the models according to the CAPRI model quality criteria. The tool can handle a variety of protein complex types including those involving peptides, nucleic acids, and oligosaccharides. The source code is freely available from https://gitlab.in2p3.fr/cmsb-public/CAPRI-Q and its web interface through the Dockground resource at https://dockground.compbio.ku.edu/assessment/. [ABSTRACT FROM AUTHOR]

The identification of many places as centres of designer shopping has in recent decades favoured a number of Italian destinations for which this aspect has become a promotional feature similar to art, landscape and food. In Campania, this phenomenon has developed particularly in Capri, Ischia and Positano, wherein the mid-twentieth century, thanks to the initiative of local craftsmen or cunning outsiders, tailor’s shops, boutiques and workshops were set up in response to customers’ demand for clothes and accessories suited to holiday life. Thus, for different reasons and in different ways, resort fashion has taken off here, a thriving national production sector, characterised by accents strongly related to the ‘knowledge’, rituals and climate of these special places. The combination of the intangible qualities which characterised the garments and the craft traditions of the localities gave rise to artefacts capable of responding to the search for new emotional sensations that belonged to the steadily increasing number of tourists, which was satisfied by environments and lifestyles that were completely different from their usual ones. This process found a decisive conjuncture in the fact that in the middle of the century fashion joined tourism and cinema to bring Italy out of the post-war crisis. And in Campania, in particular, manufacturing and cultural conditions, folklore and the rich natural heritage of the coasts were some of the main drivers of this project, favoured in this sense in Capri and Positano by ideal landscape conditions for conveying the results of the most authentic creativity.

A field experiment was conducted to assess the impact of various planting densities and levels of shoot thinning on cut flower yield, quality, soil chemical properties and cost economics in the commercially cultivated alstroemeria cultivar 'Capri'. The experiment involved three planting densities (4, 6 and 8 plants/m 2 ) along with three shoot thinning levels (10 %, 20 % and 30 %). It was observed that higher planting density (4 plants/m 2 ) promoted the length of cut stem, early bud formation, and flowering, optimal quality parameters, including maximum stem thickness, cut stem weight, floret quantity/stem, floret size, number of flowering stems/plant (yield) and vase life. Exclusive use of higher vegetative mass removal (30 % shoot thinning) was found to improve quality parameters such as the length of cut stem, number of flowering stems, stem thickness, weight of cut stem, floret quantity/stem, floret size, vase life, and early flowering. Soil samples were collected from each treatment and the consequent lab analysis revealed that the lower planting density and shoot thinning level resulted in maximum soil organic carbon, nitrogen, phosphorous and potassium content. In conclusion, planting density of 4 plants/m 2 and 30 % shoot thinning emerged as the optimal combination for enhancing quantitative parameters in commercial alstroemeria cultivation. The study underscores the importance of strategic planting practices and vegetative mass management for maximizing yield and quality in alstroemeria production, along with ensuring higher economic returns., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors.)

The sociocultural adaptation of migrants is a multifaceted historical theme, which includes many aspects from statistical indicators to the emotional aspects of adaptation. The relevance of reserching the adaptation of artistic intelligentsia is associated with the need of comprehensive analysis of this phenomenon. The article deals with the potential and the process of adaptation of the “Russian colony” on Capri in 1905-1914. The research is based on unpublished and published personal materials - memoirs and correspondence. The period between the Russian Revolution of 1905 and the beginning of the First World War was a stage in the modern consciousness of the Russian artistic intelligentsia, who felt the urgent need for renewal, but could not put it into life. The failure of the first revolution forced many of them to leave Russia, while others did it of their own free will. The article is focused on the personal perception of the artistic intelligentsia to their position as temporary migrants, the process of building interaction within a fairly large emigrant community and with the local population. The methodological base is associated with a biographical approach in historical researchers and some elements of the new cultural history. The adaptation strategy of temporary migrants was directed inside the community: the main goal was the unification of Russian emigration, the creation and maintenance of a cultural field in conditions of separation from Russia. Despite the strong demarcations within the community, maintained by the migrants themselves, mainly along ideological boundaries, subsequently the period of stay on Capri has become a special nostalgic point in the memoirs of representatives of the artistic intelligentsia and political activists.

Am 22. Januar 1891 verabschiedete Kaiser Wilhelm II in Cuxhaven den Passagierdampfer Augusta Victoria, der zwei Monate lang das Mittelmeer und einige seiner wichtigsten Städte auskundschaften sollte, und läutete damit das Zeitalter der Vergnügungs-Schifffahrten ein. An Bord waren 241 betuchte Passagiere, unter ihnen der Zeichner Ch. W. Allers, der seine Reiserinnerungen in Backschisch. Die erste deutsche Kreuzfahrt in das Mittelmeer dokumentiert und damit ein einmaliges Zeugnis über die mediterrane Faszination im imperialistischen Zeitalter abgibt. Auf der Grundlage eines eurozentrischen bzw. nationalen Gefühls wird der Mittelmeerraum von dem Mikrokosmos der deutschen Reisegesellschaft als naturräumliche und ideologische Einheit wahrgenommen. Die kulturellen Gemeinsamkeiten bestimmen dabei die Erfahrung der Fremde und vermengen vermeintlich mediterrane Spezifika mit Wunschprojektionen der Tourismuswerbung und kolonialen Propaganda.

We present the results for CAPRI Round 30, the first joint CASP-CAPRI experiment, which brought together experts from the protein structure prediction and protein-protein docking communities. The Round comprised 25 targets from amongst those submitted for the CASP11 prediction experiment of 2014. The targets included mostly homodimers, a few homotetramers, and two heterodimers, and comprised protein chains that could readily be modeled using templates from the Protein Data Bank. On average 24 CAPRI groups and 7 CASP groups submitted docking predictions for each target, and 12 CAPRI groups per target participated in the CAPRI scoring experiment. In total more than 9500 models were assessed against the 3D structures of the corresponding target complexes. Results show that the prediction of homodimer assemblies by homology modeling techniques and docking calculations is quite successful for targets featuring large enough subunit interfaces to represent stable associations. Targets with ambiguous or inaccurate oligomeric state assignments, often featuring crystal contact-sized interfaces, represented a confounding factor. For those, a much poorer prediction performance was achieved, while nonetheless often providing helpful clues on the correct oligomeric state of the protein. The prediction performance was very poor for genuine tetrameric targets, where the inaccuracy of the homology-built subunit models and the smaller pair-wise interfaces severely limited the ability to derive the correct assembly mode. Our analysis also shows that docking procedures tend to perform better than standard homology modeling techniques and that highly accurate models of the protein components are not always required to identify their association modes with acceptable accuracy. Proteins 2016; 84(Suppl 1):323-348. © 2016 Wiley Periodicals, Inc.

Protein structure docking is the process in which the quaternary structure of a protein complex is predicted from individual tertiary structures of the protein subunits. Protein docking is typically performed in two main steps. The subunits are first docked while keeping them rigid to form the complex, which is then followed by structure refinement. Structure refinement is crucial for a practical use of computational protein docking models, as it is aimed for correcting conformations of interacting residues and atoms at the interface. Here, we benchmarked the performance of eight existing protein structure refinement methods in refinement of protein complex models. We show that the fraction of native contacts between subunits is by far the most straightforward metric to improve. However, backbone dependent metrics, based on the Root Mean Square Deviation proved more difficult to improve via refinement. [ABSTRACT FROM AUTHOR]

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We present the results for CAPRI Round 50, the fourth joint CASP‐CAPRI protein assembly prediction challenge. The Round comprised a total of twelve targets, including six dimers, three trimers, and three higher‐order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher‐order oligomers). Eight were difficult targets for which only distantly related templates were found for the individual subunits. Twenty‐five CAPRI groups including eight automatic servers submitted ~1250 models per target. Twenty groups including six servers participated in the CAPRI scoring challenge submitted ~190 models per target. The accuracy of the predicted models was evaluated using the classical CAPRI criteria. The prediction performance was measured by a weighted scoring scheme that takes into account the number of models of acceptable quality or higher submitted by each group as part of their five top‐ranking models. Compared to the previous CASP‐CAPRI challenge, top performing groups submitted such models for a larger fraction (70–75%) of the targets in this Round, but fewer of these models were of high accuracy. Scorer groups achieved stronger performance with more groups submitting correct models for 70–80% of the targets or achieving high accuracy predictions. Servers performed less well in general, except for the MDOCKPP and LZERD servers, who performed on par with human groups. In addition to these results, major advances in methodology are discussed, providing an informative overview of where the prediction of protein assemblies currently stands. [ABSTRACT FROM AUTHOR]

Diseases caused by bacterial infections become a critical problem in public heath. Antibiotic, the traditional treatment, gradually loses their effectiveness due to the resistance. Meanwhile, antibacterial proteins attract more attention because of broad spectrum and little harm to host cells. Therefore, exploring new effective antibacterial proteins is urgent and necessary. In this paper, we are committed to evaluating the effectiveness of ab-initio docking methods in antibacterial protein–protein docking. For this purpose, we constructed a three-dimensional (3D) structure dataset of antibacterial protein complex, called APCset, which contained |$19$| protein complexes whose receptors or ligands are homologous to antibacterial peptides from Antimicrobial Peptide Database. Then we selected five representative ab-initio protein–protein docking tools including ZDOCK3.0.2, FRODOCK3.0, ATTRACT, PatchDock and Rosetta to identify these complexes' structure, whose performance differences were obtained by analyzing from five aspects, including top/best pose, first hit, success rate, average hit count and running time. Finally, according to different requirements, we assessed and recommended relatively efficient protein–protein docking tools. In terms of computational efficiency and performance, ZDOCK was more suitable as preferred computational tool, with average running time of |$6.144$| minutes, average Fnat of best pose of |$0.953$| and average rank of best pose of |$4.158$|⁠. Meanwhile, ZDOCK still yielded better performance on Benchmark 5.0, which proved ZDOCK was effective in performing docking on large-scale dataset. Our survey can offer insights into the research on the treatment of bacterial infections by utilizing the appropriate docking methods. [ABSTRACT FROM AUTHOR]

Neutrophils sense and migrate through an enormous range of chemoattractant gradients through adaptation. Here, we reveal that in human neutrophils, calcium-promoted Ras inactivator (CAPRI) locally controls the GPCR-stimulated Ras adaptation. Human neutrophils lacking CAPRI (caprikd) exhibit chemoattractant-induced, nonadaptive Ras activation; significantly increased phosphorylation of AKT, GSK-3α/3β, and cofilin; and excessive actin polymerization. caprikd cells display defective chemotaxis in response to high-concentration gradients but exhibit improved chemotaxis in low- or subsensitive-concentration gradients of various chemoattractants, as a result of their enhanced sensitivity. Taken together, our data reveal that CAPRI controls GPCR activation-mediated Ras adaptation and lowers the sensitivity of human neutrophils so that they are able to chemotax through a higher-concentration range of chemoattractant gradients. [ABSTRACT FROM AUTHOR]

• Rediscovery of monumental olive trees in Capri Island. • Unknown olive cultivars increasing the diversity of olive germplasm. • Route of olive cultivation from Ancient Greece to Italy. • Recovery of abandoned olive groves against the soil erosion. • Enhance the intangible cultural heritage close to extinction. The ancient olive trees are the living proof of the very long tradition of cultivation, and, in most cases, their genotyping has revealed strong differences with the actual known olive varieties. Thus, in addition to their historical and cultural significance, old olives offer horticultural interest due to their genetic potential, constituting an un-exploited reservoir of olive diversity. Moreover, in the last decades several ancient orchards were abandoned generating dramatic scenarios at social, landscape and biodiversity levels. To highlight the importance of abandoned olive trees, a deep restoration was made in an Island well known for the tourism as Capri, which was important in the past for agropastoral activities. The different morphologies detected after orchards cleaning together with the huge dimensions of some olive trees, had open the possibility to seek for the ancient olive cultivation in the Capri Island. The molecular identification of both canopy and rootstock through SSR markers of 67 accessions, highlight the existence of twenty-one ancient genotypes in this island. Two of these were corresponded to the Italian and Greek known cultivars while the genetic identity of remained genotypes resulted unique, even have been compared genetically with more than 450 worldwide olive cultivars. Molecular identification has demonstrated that some of them were clonally propagated and only in two cases, the grafting scenario has been discovered. Age determination by radiocarbon (14C) dating and specific algebraic formulas, shed light on the centennial age of analyzed trees, meaning that they probably represent remnants of ancient olive cultivations, since hundreds of years ago. The outstanding performance of these trees makes really promising their agronomical evaluation and possible use in future olive breeding programs. Their ongoing propagation will avoid losing this priceless olive germplasm and will re-constitute olive orchards with autochthonous and well-adapted varieties in the Capri Island restarting the extra virgin olive oil production after decades of abandonment. [ABSTRACT FROM AUTHOR]

In recent years the issue of touristification has been progressively discussed in relation to its impact on historic towns. In this regard, physical transformations and gentrification consequences are both issues often addressed. In Italy, consciousness on the subject primarily grew in relation to Florence and Venice, both national cases widely discussed also on newspapers. The awareness of a wider range of cases affected by this problem, from big cities to small holiday destinations, is even more recent. The aim of the present paper is to address Capri’s touristification process, which started in the last decades of the nineteenth century and exploded in the second half of the twentieth century, from the point of view of the field of study of history and conservation of cultural heritage and landscape. Therefore, this process and some of its consequences on the island’s cultural landscape and identity are thoroughly analyzed. The paper starts with a brief introduction to the island and its history, which is necessary in order to highlight its rich cultural heritage and the slow pace at which Capri has grown over time as a fishermen island to suddenly transforming into a touristic destination during the last century. Finally, the current touristic vocation and the consequences on Capri’s natural and built environment are discussed, with the aim of individuating if and why there have already been losses and what should be done to prevent this negative process from going on.

Abstract Background Molecular docking studies on protein-peptide interactions are a challenging and time-consuming task because peptides are generally more flexible than proteins and tend to adopt numerous conformations. There are several benchmarking studies on protein-protein, protein-ligand and nucleic acid-ligand docking interactions. However, a series of docking methods is not rigorously validated for protein-peptide complexes in the literature. Considering the importance and wide application of peptide docking, we describe benchmarking of 6 docking methods on 133 protein-peptide complexes having peptide length between 9 to 15 residues. The performance of docking methods was evaluated using CAPRI parameters like FNAT, I-RMSD, L-RMSD. Result Firstly, we performed blind docking and evaluate the performance of the top docking pose of each method. It was observed that FRODOCK performed better than other methods with average L-RMSD of 12.46 Å. The performance of all methods improved significantly for their best docking pose and achieved highest average L-RMSD of 3.72 Å in case of FRODOCK. Similarly, we performed re-docking and evaluated the performance of the top and best docking pose of each method. We achieved the best performance in case of ZDOCK with average L-RMSD 8.60 Å and 2.88 Å for the top and best docking pose respectively. Methods were also evaluated on 40 protein-peptide complexes used in the previous benchmarking study, where peptide have length up to 5 residues. In case of best docking pose, we achieved the highest average L-RMSD of 4.45 Å and 2.09 Å for the blind docking using FRODOCK and re-docking using AutoDock Vina respectively. Conclusion The study shows that FRODOCK performed best in case of blind docking and ZDOCK in case of re-docking. There is a need to improve the ranking of docking pose generated by different methods, as the present ranking scheme is not satisfactory. To facilitate the scientific community for calculating CAPRI parameters between native and docked complexes, we developed a web-based service named PPDbench (http://webs.iiitd.edu.in/raghava/ppdbench/).

In the last decades a large number of Italian tourist destinations have become increasingly popular thanks to the growth of purchase as a consolidated habit of collective tourism, and to the identification of many sites as upscale shopping centers. For such resorts, this trend has turned into a tool for promotion comparable to art, landscape and food. This phenomenon developed in particular in Capri, Ischia and Positano, where between the Fifties and Sixties, thanks to the initiative of local artisans or shrewd foreigner visitors, tailor’s shops, boutiques and workshops were created in response to the customers’ requests for clothes and accessories tuned to the native ‘style’. The authenticity of this process was originally guaranteed by the strong consolidated artisan tradition of the sites and found a favorable conjuncture in the fact that in the middle of the century fashion was combined with tourism and cinema to help Italy out of the post-war crisis. Thanks to its folklore and natural landscape heritage connected to the beauty of its coast, Naples acted as a main trigger for this project: it boasted suitable productive, cultural and economic conditions to aspire to become the "capital of fashion in southern Italy" and Capri, Ischia and Positano were the ideal stages through which the new facet of Italian creativity could be conveyed.

The UK exited the EU on 31 January 2020, with a transition period agreed as part of the Withdrawal Agreement. During this transition period the UK and the EU will decide on their future trading relationship. No matter what form this relationship takes, there will be disturbances to agri‐food markets. This study analyses four different scenarios with increasing barriers to trade, ranging from a very close relationship similar to the European Economic Area to a distant relationship in which the UK and EU trade on Most Favoured Nation terms, using the EU focused global agricultural sector model CAPRI. In the UK, food prices will increase in all scenarios, making consumers in the UK the biggest losers. Only in a free trade agreement scenario does the UK show an unambiguous positive net welfare gain in just the agri‐food sector. In the case of the European Economic Area scenario, which assumes continued access to the single market, the net welfare impact would depend on the size of the UK's continued contribution to the EU. In the EU, declining food prices would benefit consumers but the sum of the loss in farmers' incomes and the UK's EU CAP contribution would be much greater than the consumer's gain. These impacts in agricultural markets under different future trade arrangements will also be influenced by the UK's agricultural policy changes in direct payments as well as by possible further UK trade liberalisation after the end of the transition period. [ABSTRACT FROM AUTHOR]

Protein‐protein docking plays an important role in the computational prediction of the complex structure between two proteins. For years, a variety of docking algorithms have been developed, as witnessed by the critical assessment of prediction interactions (CAPRI) experiments. However, despite their successes, many docking algorithms often require a series of manual operations like modeling structures from sequences, incorporating biological information, and selecting final models. The difficulties in these manual steps have significantly limited the applications of protein‐protein docking, as most of the users in the community are nonexperts in docking. Therefore, automated docking like a web server, which can give a comparable performance to human docking protocol, is pressingly needed. As such, we have participated in the blind CAPRI experiments for Rounds 38‐45 and CASP13‐CAPRI challenge for Round 46 with both our HDOCK automated docking web server and human docking protocol. It was shown that our HDOCK server achieved an "acceptable" or higher CAPRI‐rated model in the top 10 submitted predictions for 65.5% and 59.1% of the targets in the docking experiments of CAPRI and CASP13‐CAPRI, respectively, which are comparable to 66.7% and 54.5% for human docking protocol. Similar trends can also be observed in the scoring experiments. These results validated our HDOCK server as an efficient automated docking protocol for nonexpert users. Challenges and opportunities of automated docking are also discussed. [ABSTRACT FROM AUTHOR]

Protein docking algorithms aim to predict the 3D structure of a protein complex from the structures of its separated components. In the past, most docking algorithms focused on docking pairs of proteins to form dimeric complexes. However, attention is now turning towards the more difficult problem of using docking methods to predict the structures of multicomponent complexes. In both cases, however, the constituent proteins often change conformation upon complex formation, and this can cause many algorithms to fail to detect near‐native binding orientations due to the high number of atomic steric clashes in the list of candidate solutions. An increasingly popular way to retain more near‐native orientations is to define one or more restraints that serve to modulate or override the effect of steric clashes. Here, we present an updated version of our "EROS‐DOCK" docking algorithm which has been extended to dock arbitrary dimeric and trimeric complexes, and to allow the user to define residue‐residue or atom‐atom interaction restraints. Our results show that using even just one residue‐residue restraint in each interaction interface is sufficient to increase the number of cases with acceptable solutions within the top 10 from 51 to 121 out of 173 pairwise docking cases, and to successfully dock 8 out of 11 trimeric complexes. [ABSTRACT FROM AUTHOR]

Integration of template‐based modeling, global sampling and precise scoring is crucial for the development of molecular docking programs with improved accuracy. We combined template‐based modeling and ab‐initio docking protocol as hybrid docking strategy called CoDock for the docking and scoring experiments of the seventh CAPRI edition. For CAPRI rounds 38‐45, we obtained acceptable or better models in the top 10 submissions for eight out of the 16 evaluated targets as predictors, nine out of the 16 targets as scorers. Especially, we submitted acceptable models for all of the evaluated protein‐oligosaccharide targets. For the CASP13‐CAPRI experiment (round 46), we obtained acceptable or better models in the top 5 submissions for 10 out of the 20 evaluated targets as predictors, 11 out of the 20 targets as scorers. The failed cases for our group were mainly the difficult targets and the protein‐peptide systems in CAPRI and CASP13‐CAPRI experiments. In summary, this CAPRI edition showed that our hybrid docking strategy can be efficiently adapted to the increasing variety of challenges in the field of molecular interactions. [ABSTRACT FROM AUTHOR]

We present the seventh report on the performance of methods for predicting the atomic resolution structures of protein complexes offered as targets to the community‐wide initiative on the Critical Assessment of Predicted Interactions. Performance was evaluated on the basis of 36 114 models of protein complexes submitted by 57 groups—including 13 automatic servers—in prediction rounds held during the years 2016 to 2019 for eight protein‐protein, three protein‐peptide, and five protein‐oligosaccharide targets with different length ligands. Six of the protein‐protein targets represented challenging hetero‐complexes, due to factors such as availability of distantly related templates for the individual subunits, or for the full complex, inter‐domain flexibility, conformational adjustments at the binding region, or the multi‐component nature of the complex. The main challenge for the protein‐peptide and protein‐oligosaccharide complexes was to accurately model the ligand conformation and its interactions at the interface. Encouragingly, models of acceptable quality, or better, were obtained for a total of six protein‐protein complexes, which included four of the challenging hetero‐complexes and a homo‐decamer. But fewer of these targets were predicted with medium or higher accuracy. High accuracy models were obtained for two of the three protein‐peptide targets, and for one of the protein‐oligosaccharide targets. The remaining protein‐sugar targets were predicted with medium accuracy. Our analysis indicates that progress in predicting increasingly challenging and diverse types of targets is due to closer integration of template‐based modeling techniques with docking, scoring, and model refinement procedures, and to significant incremental improvements in the underlying methodologies. [ABSTRACT FROM AUTHOR]

The seventh CAPRI edition imposed new challenges to the modeling of protein‐protein complexes, such as multimeric oligomerization, protein‐peptide, and protein‐oligosaccharide interactions. Many of the proposed targets needed the efficient integration of rigid‐body docking, template‐based modeling, flexible optimization, multiparametric scoring, and experimental restraints. This was especially relevant for the multimolecular assemblies proposed in the CASP12‐CAPRI37 and CASP13‐CAPRI46 joint rounds, which were described and evaluated elsewhere. Focusing on the purely CAPRI targets of this edition (rounds 38‐45), we have participated in all 17 assessed targets (considering heteromeric and homomeric interfaces in T125 as two separate targets) both as predictors and as scorers, by using integrative modeling based on our docking and scoring approaches: pyDock, IRaPPA, and LightDock. In the protein‐protein and protein‐peptide targets, we have also participated with our webserver (pyDockWeb). On these 17 CAPRI targets, we submitted acceptable models (or better) within our top 10 models for 10 targets as predictors, 13 targets as scorers, and 4 targets as servers. In summary, our participation in this CAPRI edition confirmed the capabilities of pyDock for the scoring of docking models, increasingly used within the context of integrative modeling of protein interactions and multimeric assemblies. [ABSTRACT FROM AUTHOR]

Critical Assessment of PRediction of Interactions (CAPRI) rounds 37 through 45 introduced larger complexes, new macromolecules, and multistage assemblies. For these rounds, we used and expanded docking methods in Rosetta to model 23 target complexes. We successfully predicted 14 target complexes and recognized and refined near‐native models generated by other groups for two further targets. Notably, for targets T110 and T136, we achieved the closest prediction of any CAPRI participant. We created several innovative approaches during these rounds. Since round 39 (target 122), we have used the new RosettaDock 4.0, which has a revamped coarse‐grained energy function and the ability to perform conformer selection during docking with hundreds of pregenerated protein backbones. Ten of the complexes had some degree of symmetry in their interactions, so we tested Rosetta SymDock, realized its shortcomings, and developed the next‐generation symmetric docking protocol, SymDock2, which includes docking of multiple backbones and induced‐fit refinement. Since the last CAPRI assessment, we also developed methods for modeling and designing carbohydrates in Rosetta, and we used them to successfully model oligosaccharide‐protein complexes in round 41. Although the results were broadly encouraging, they also highlighted the pressing need to invest in (a) flexible docking algorithms with the ability to model loop and linker motions and in (b) new sampling and scoring methods for oligosaccharide‐protein interactions. [ABSTRACT FROM AUTHOR]

Computational structural prediction of macromolecular interactions is a fundamental tool toward the global understanding of cellular processes. The Critical Assessment of PRediction of Interactions (CAPRI) community‐wide experiment provides excellent opportunities for blind testing computational docking methods and includes original targets, thus widening the range of docking applications. Our participation in CAPRI rounds 38 to 45 enabled us to expand the way we include evolutionary information in structural predictions beyond our standard free docking InterEvDock pipeline. InterEvDock integrates a coarse‐grained potential that accounts for interface coevolution based on joint multiple sequence alignments of two protein partners (co‐alignments). However, even though such co‐alignments could be built for none of the CAPRI targets in rounds 38 to 45, including host‐pathogen and protein‐oligosaccharide complexes and a redesigned interface, we identified multiple strategies that can be used to incorporate evolutionary constraints, which helped us to identify the most likely macromolecular binding modes. These strategies include template‐based modeling where only local adjustments should be applied when query‐template sequence identity is above 30% and larger perturbations are needed below this threshold; covariation‐based structure prediction for individual protein partners; and the identification of evolutionarily conserved and structurally recurrent anchoring interface motifs. Overall, we submitted correct predictions among the top 5 models for 12 out of 19 interface challenges, including four High‐ and five Medium‐quality predictions. Our top 20 models included correct predictions for three out of the five targets we missed in the top 5, including two targets for which misleading biological data led us to downgrade correct free docking models. [ABSTRACT FROM AUTHOR]

The formation of specific protein‐protein interactions is often a key to a protein's function. During complex formation, each protein component will undergo a change in the conformational state, for some these changes are relatively small and reside primarily at the sidechain level; however, others may display notable backbone adjustments. One of the classic problems in the protein‐docking field is to be able to a priori predict the extent of such conformational changes. In this work, we investigated three protocols to find the most suitable input structure conformations for cross‐docking, including a robust sampling approach in normal mode space. Counterintuitively, knowledge of the theoretically best combination of normal modes for unbound‐bound transitions does not always lead to the best results. We used a novel spatial partitioning library, Aether Engine (see Supplementary Materials), to efficiently search the conformational states of 56 receptor/ligand pairs, including a recent CAPRI target, in a systematic manner and selected diverse conformations as input to our automated docking server, SwarmDock, a server that allows moderate conformational adjustments during the docking process. In essence, here we present a dynamic cross‐docking protocol, which when benchmarked against the simpler approach of just docking the unbound components shows a 10% uplift in the quality of the top docking pose. [ABSTRACT FROM AUTHOR]

We report the performance of the protein docking prediction pipeline of our group and the results for Critical Assessment of Prediction of Interactions (CAPRI) rounds 38‐46. The pipeline integrates programs developed in our group as well as other existing scoring functions. The core of the pipeline is the LZerD protein‐protein docking algorithm. If templates of the target complex are not found in PDB, the first step of our docking prediction pipeline is to run LZerD for a query protein pair. Meanwhile, in the case of human group prediction, we survey the literature to find information that can guide the modeling, such as protein‐protein interface information. In addition to any literature information and binding residue prediction, generated docking decoys were selected by a rank aggregation of statistical scoring functions. The top 10 decoys were relaxed by a short molecular dynamics simulation before submission to remove atom clashes and improve side‐chain conformations. In these CAPRI rounds, our group, particularly the LZerD server, showed robust performance. On the other hand, there are failed cases where some other groups were successful. To understand weaknesses of our pipeline, we analyzed sources of errors for failed targets. Since we noted that structure refinement is a step that needs improvement, we newly performed a comparative study of several refinement approaches. Finally, we show several examples that illustrate successful and unsuccessful cases by our group. [ABSTRACT FROM AUTHOR]

This work evaluated the difference in dosimetry of high dose rate (HDR) brachytherapy treatments between plans using advanced multichannel applicators and simplified base versions. Eighteen HDR patients treated using Interstitial Ring CT/MR Applicator Set (Elekta Brachytherapy, Netherlands) (TRN) (21 plans), CapriTM Applicator Set (Varian Medical Systems, Inc., Palo Alto, CA) (CC) (19 plans), Rotte Endometrial Applicator Set (Elekta Brachytherapy, Netherlands) (RDT) (18 plans), and the Advanced Gynecological Applicator Venezia (Vz) (Elekta Brachytherapy, Netherlands) (6 plans) were retrospectively reviewed. For each plan, "advanced" channels including any interstitial channels, the 12 noncentral channels in the CC, and the lateral extending aspects of the RDT were removed and a new plan with the original inverse planning settings was optimized using only the remaining "simplified" applicator and compared to the original. The new plans were renormalized to match the original percent dose to 90% of the high-risk clinical target volume (HR-CTV). Critical structures included bladder, rectum, sigmoid colon, and small bowel. Comparisons were made utilizing dose volume histograms of HR-CTVs, conformation number (CN), and the equivalent total dose in 2 Gy fractions (EQD2) to 2 cm3 of the normal structures. Comparing simplified to advanced plans, the average percent differences in EQD2 to 2 cm3 for Vz, with 95% confidence interval, were 101.7 ± 85.9%, 147.8 ± 76.7%, 95.3 ± 61.6%, and 44.0 ± 12.4% for Rectum, Bladder, Sigmoid, and Bowel, respectively. For TRN: 36.9 ± 18.5%, 38.2 ± 14.5%, 20.3 ± 8.8%, and 15.3 ± 8.2%. For CC: 18.9 ± 3.7%, 12.3 ± 5.3%, 27.8 ± 7.1%, and 17.1 ± 3.6%. For RDT: 1.5 ± 6.8%, 7.4 ± 6.7%, 11.1 ± 4.4%, and 8.0 ± 8.7%. The CN was better in advanced applications by 0.024 for RDT, 0.104 for TRN, 0.043 for CC, and 0.251 for Vz (all p < 0.05). Advanced multichannel treatments allow better target dose conformation and normal tissue dose manipulation. The biggest factors influencing the brachytherapy dose distributions are the number of available channels and their separation from each other within the target. [ABSTRACT FROM AUTHOR]

We present the results for CAPRI Round 46, the third joint CASP‐CAPRI protein assembly prediction challenge. The Round comprised a total of 20 targets including 14 homo‐oligomers and 6 heterocomplexes. Eight of the homo‐oligomer targets and one heterodimer comprised proteins that could be readily modeled using templates from the Protein Data Bank, often available for the full assembly. The remaining 11 targets comprised 5 homodimers, 3 heterodimers, and two higher‐order assemblies. These were more difficult to model, as their prediction mainly involved "ab‐initio" docking of subunit models derived from distantly related templates. A total of ~30 CAPRI groups, including 9 automatic servers, submitted on average ~2000 models per target. About 17 groups participated in the CAPRI scoring rounds, offered for most targets, submitting ~170 models per target. The prediction performance, measured by the fraction of models of acceptable quality or higher submitted across all predictors groups, was very good to excellent for the nine easy targets. Poorer performance was achieved by predictors for the 11 difficult targets, with medium and high quality models submitted for only 3 of these targets. A similar performance "gap" was displayed by scorer groups, highlighting yet again the unmet challenge of modeling the conformational changes of the protein components that occur upon binding or that must be accounted for in template‐based modeling. Our analysis also indicates that residues in binding interfaces were less well predicted in this set of targets than in previous Rounds, providing useful insights for directions of future improvements. [ABSTRACT FROM AUTHOR]

Proteins frequently interact with each other, and the knowledge of structures of the corresponding protein complexes is necessary to understand how they function. Computational methods are increasingly used to provide structural models of protein complexes. Not surprisingly, community‐wide Critical Assessment of protein Structure Prediction (CASP) experiments have recently started monitoring the progress in this research area. We participated in CASP13 with the aim to evaluate our current capabilities in modeling of protein complexes and to gain a better understanding of factors that exert the largest impact on these capabilities. To model protein complexes in CASP13, we applied template‐based modeling, free docking and hybrid techniques that enabled us to generate models of the topmost quality for 27 of 42 multimers. If templates for protein complexes could be identified, we modeled the structures with reasonable accuracy by straightforward homology modeling. If only partial templates were available, it was nevertheless possible to predict the interaction interfaces correctly or to generate acceptable models for protein complexes by combining template‐based modeling with docking. If no templates were available, we used rigid‐body docking with limited success. However, in some free docking models, despite the incorrect subunit orientation and missed interface contacts, the approximate location of protein binding sites was identified correctly. Apparently, our overall performance in docking was limited by the quality of monomer models and by the imperfection of scoring methods. The impact of human intervention on our results in modeling of protein complexes was significant indicating the need for improvements of automatic methods. [ABSTRACT FROM AUTHOR]

Comparing accuracies of structural protein-protein interaction (PPI) models for different complexes on an absolute scale is a challenge, requiring normalization of scores across structures of different sizes and shapes. To help address this challenge, we have developed a statistical significance metric for docking models, called random-docking (RD) p-value. This score evaluates a PPI model based on how likely a random docking process is to produce a model of better or equal accuracy. The binding partners are randomly docked against each other a large number of times, and the probability of sampling a model of equal or greater accuracy from this reference distribution is the RD p-value. Using a subset of top predicted models from CAPRI (Critical Assessment of PRediction of Interactions) rounds over 2017-2020, we find that the ease of achieving a given root mean squared deviation or DOCKQ score varies considerably by target; achieving the same relative metric can be thousands of times easier for one complex compared to another. In contrast, RD p-values inherently normalize scores for models of different complexes, making them globally comparable. Furthermore, one can calculate RD p-values after generating a reference distribution that accounts for prior information about the interface geometry, such as residues involved in binding, by giving the random-docking process access the same information. Thus, one can decouple improvements in prediction accuracy that arise solely from basic modeling constraints from those due to the rest of the method. We provide efficient code for computing RD p-values at https://github.com/Grigoryanlab/RDP., (© 2023 The Protein Society.)

The Common Agricultural Policy of the European Union (CAP) is one of the oldest and most controversial of the UE policies. Different possible scenarios of the future reforms of the CAP are currently being discussed. They vary in terms of the extent and the type of the intervention and consequently the welfare effects for different social groups. The objective of this paper is to demonstrate that the partial equilibrium model (CAPRI) and the Theory of Moves (TOM) can be jointly used to test socio-political acceptance of the CAP's reforms, informing subsequent changes to the policy. Our exemplary results demonstrate that liquidation of the first pillar of the CAP would negatively influence the socio-political acceptance of the CAP. [ABSTRACT FROM AUTHOR]

Background: Molecular docking studies on protein-peptide interactions are a challenging and time-consuming task because peptides are generally more flexible than proteins and tend to adopt numerous conformations. There are several benchmarking studies on protein-protein, protein-ligand and nucleic acid-ligand docking interactions. However, a series of docking methods is not rigorously validated for protein-peptide complexes in the literature. Considering the importance and wide application of peptide docking, we describe benchmarking of 6 docking methods on 133 protein-peptide complexes having peptide length between 9 to 15 residues. The performance of docking methods was evaluated using CAPRI parameters like FNAT, I-RMSD, L-RMSD. Result: Firstly, we performed blind docking and evaluate the performance of the top docking pose of each method. It was observed that FRODOCK performed better than other methods with average L-RMSD of 12.46 Å. The performance of all methods improved significantly for their best docking pose and achieved highest average L-RMSD of 3.72 Å in case of FRODOCK. Similarly, we performed re-docking and evaluated the performance of the top and best docking pose of each method. We achieved the best performance in case of ZDOCK with average L-RMSD 8.60 Å and 2.88 Å for the top and best docking pose respectively. Methods were also evaluated on 40 protein-peptide complexes used in the previous benchmarking study, where peptide have length up to 5 residues. In case of best docking pose, we achieved the highest average L-RMSD of 4.45 Å and 2.09 Å for the blind docking using FRODOCK and re-docking using AutoDock Vina respectively. Conclusion: The study shows that FRODOCK performed best in case of blind docking and ZDOCK in case of re-docking. There is a need to improve the ranking of docking pose generated by different methods, as the present ranking scheme is not satisfactory. To facilitate the scientific community for calculating CAPRI parameters between native and docked complexes, we developed a web-based service named PPDbench (http://webs.iiitd.edu.in/raghava/ppdbench/). [ABSTRACT FROM AUTHOR]

Conrad inspired seven memoirs, published between 1926 and 1981, by his wife Jessie, his two sons (Borys and John) and three colleagues who knew him well: Ford Madox Ford, Richard Curle, and Joseph Retinger. Their viewpoints range from reverence and awe to condescension and hostility. Torn between focusing on Conrad and telling their own story, the memoirs are personally biased, have a strong element of self-interest and reveal more about the authors than the subject. No matter how inaccurate or self-aggrandizing, these memoirs are valuable sources for his biographers, who mine the gold and reject the dross, correct the errors and establish the truth. They describe domestic details, narrate important events in his life, reveal his strange character and portray the culture in which he lived, competing in trying to present the authoritative view of Conrad. [136 words] [ABSTRACT FROM AUTHOR]

The main problems of the development of heavy oil fields and the ways of their solution are considered. The modern nontraditional methods for extracting heavy crude oils, ensuring their in situ upgrading, such as aquathermolysis, combination of catalytic upgrading and in situ combustion, and in situ electric heating, are analyzed. Research fields that could bring the technologies for heavy crude oil extraction closer to the ready-touse level are outlined. The main processes allowing heavy crude oil to be involved in processing at the existing oil refineries are considered, and the Russian experience in this field is demonstrated. [ABSTRACT FROM AUTHOR]

In view of the increasing interest both in inhibitors of protein-protein interactions and in protein drugs themselves, analysis of the three-dimensional structure of protein-protein complexes is assuming greater relevance in drug design. In the many cases where an experimental structure is not available, protein-protein docking becomes the method of choice for predicting the arrangement of the complex. However, reliably scoring protein-protein docking poses is still an unsolved problem. As a consequence, the screening of many docking models is usually required in the analysis step, to possibly single out the correct ones. Here, making use of exemplary cases, we review our recently introduced methods for the analysis of protein complex structures and for the scoring of protein docking poses, based on the use of inter-residue contacts and their visualization in inter-molecular contact maps. We also show that the ensemble of tools we developed can be used in the context of rational drug design targeting protein-protein interactions.