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201. Molsurfer: two-dimensional maps for navigating three-dimensional structures of proteins

Author

Gabdoulline, Razif R., Wade, Rebecca C., and Walther, Dirk

Subjects
Protein research, Biological sciences, Chemistry
Abstract

A Java-based software that is capable of projecting two-dimensional protein interface maps has been developed. The software, called the MolSurfer, can be applied in the study of three-dimensional protein complexes such as biomacromolecules. MolSurfer, designed specifically for the study of intermolecular interaction among proteins, uses the ADSI-generated protein-protein interface and the Java-based PDB viewer known as WebMol.

Published
1999

211. Estimation of Drug-Target Residence Times by τ-Random Acceleration Molecular Dynamics Simulations

Author

Kokh, Daria B., primary, Amaral, Marta, additional, Bomke, Joerg, additional, Grädler, Ulrich, additional, Musil, Djordje, additional, Buchstaller, Hans-Peter, additional, Dreyer, Matthias K., additional, Frech, Matthias, additional, Lowinski, Maryse, additional, Vallee, Francois, additional, Bianciotto, Marc, additional, Rak, Alexey, additional, and Wade, Rebecca C., additional

Published
2018
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219. Comparative mapping of on-targets and off-targets for the discovery of anti-trypanosomatid folate pathway inhibitors

Author

Panecka-Hofman, Joanna, primary, Pöhner, Ina, additional, Spyrakis, Francesca, additional, Zeppelin, Talia, additional, Di Pisa, Flavio, additional, Dello Iacono, Lucia, additional, Bonucci, Alessio, additional, Quotadamo, Antonio, additional, Venturelli, Alberto, additional, Mangani, Stefano, additional, Costi, Maria Paola, additional, and Wade, Rebecca C., additional

Published
2017
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220. ENHANCED BY ENGINEERING.

Author

Wade, Rebecca

Subjects
CIVIL engineers, ENVIRONMENTAL engineering, EXPERTISE, ENGINEERING, GEOGRAPHY
Abstract

The article discusses International Women in Engineering Day (INWED) and the need to raise the profile of women engineers. It highlights the low representation of women in the engineering and technology workforce in the UK, with a decrease from 16.5% to 15.7% in 2023. The author, who is a Senior Lecturer in Environmental Science, shares her personal experience working with civil engineers to enhance local environments and promote sustainability. She also mentions her participation in the Homeward Bound International Women in Stem Leadership Programme and emphasizes the importance of collaboration and equal representation in engineering. [Extracted from the article]

Published
2024

222. Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

Author

Lensink, Marc F., Velankar, Sameer, Kryshtafovych, Andriy, Huang, Shen You, Schneidman-Duhovny, Dina, Sali, Andrej, Segura, Joan, Fernandez-Fuentes, Narcis, Viswanath, Shruthi, Elber, Ron, Grudinin, Sergei, Popov, Petr, Neveu, Emilie, Lee, Hasup, Baek, Minkyung, Park, Sangwoo, Heo, Lim, Lee, Gyu Rie, Seok, Chaok, Qin, Sanbo, Zhou, Huan Xiang, Ritchie, David W., Maigret, Bernard, Devignes, Marie Dominique, Ghoorah, Anisah, Torchala, Mieczyslaw, Chaleil, Raphaël A.G., Bates, Paul A., Ben-Zeev, Efrat, Eisenstein, Miriam, Negi, Surendra S., Weng, Zhiping, Vreven, Thom, Pierce, Brian G., Borrman, Tyler M., Yu, Jinchao, Ochsenbein, Françoise, Guerois, Raphaël, Vangone, Anna, Rodrigues, João P.G.L.M., Van Zundert, Gydo, Nellen, Mehdi, Xue, Li, Karaca, Ezgi, Melquiond, Adrien S.J., Visscher, Koen, Kastritis, Panagiotis L., Bonvin, Alexandre M.J.J., Xu, Xianjin, Qiu, Liming, Yan, Chengfei, Li, Jilong, Ma, Zhiwei, Cheng, Jianlin, Zou, Xiaoqin, Shen, Yang, Peterson, Lenna X., Kim, Hyung Rae, Roy, Amit, Han, Xusi, Esquivel-Rodriguez, Juan, Kihara, Daisuke, Yu, Xiaofeng, Bruce, Neil J., Fuller, Jonathan C., Wade, Rebecca C., Anishchenko, Ivan, Kundrotas, Petras J., Vakser, Ilya A., Imai, Kenichiro, Yamada, Kazunori, Oda, Toshiyuki, Nakamura, Tsukasa, Tomii, Kentaro, Pallara, Chiara, Romero-Durana, Miguel, Jiménez-García, Brian, Moal, Iain H., Férnandez-Recio, Juan, Joung, Jong Young, Kim, Jong Yun, Joo, Keehyoung, Lee, Jooyoung, Kozakov, Dima, Vajda, Sandor, Mottarella, Scott, Hall, David R., Beglov, Dmitri, Mamonov, Artem, Xia, Bing, Bohnuud, Tanggis, Del Carpio, Carlos A., Ichiishi, Eichiro, Marze, Nicholas, Kuroda, Daisuke, Roy Burman, Shourya S., Gray, Jeffrey J., Chermak, Edrisse, Cavallo, Luigi, Oliva, Romina, Tovchigrechko, Andrey, Wodak, Shoshana J., Molecular and Computational Toxicology, and AIMMS

Subjects
Protein docking, CASP, Protein interaction, SDG 1 - No Poverty, Oligomer state, Blind prediction, CAPRI
Abstract

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.

Published
2016

223. On the contributions of diffusion and thermal activation to electron transfer between Phormidium laminosum plastocyanin and cytochrome f: Brownian dynamics simulations with explicit modeling of nonpolar desolvation interactions and electron transfer events

Author

Gabdoulline, Razif R. and Wade, Rebecca C.

Subjects
Brownian motion -- Analysis, Cyanobacteria -- Physiological aspects, Cytochromes -- Structure, Cytochromes -- Chemical properties, Electron transport -- Analysis, Chemistry
Abstract

A detailed model of electron transfer (ET) events that was applied to all of the generated protein configurations was used to compute ET rates and understand Brownian dynamics simulations of the diffusional association of plastocyanin (PC) and cytochrome f (CytF) from the cyanobacterium Phormidium laminosum. The simulations offer insight into the strong electrostatic interactions between P. laminosum PC and CytF which influenced the ET rates from both diffusion and thermal activation processes.

Published
2009

224. Comparison of the binding and reactivity of plant and mammalian peroxidases to indole derivatives by computational docking

Author

Hallingback, Henrik R., Gabdoulline, Razif R., and Wade, Rebecca C.

Subjects
Melatonin -- Structure, Melatonin -- Properties, Crystallography -- Analysis, Oxidation-reduction reaction -- Analysis, Biological sciences, Chemistry
Abstract

A comparison of the binding and reactivity of plant and mammalian peroxidases to indole derivatives by computational docking is presented. The differentially lowered reaction rates of co II of horseradish peroxidase (HRP) and myeloperoxidase (MPO) with respect to those of co I might stem from as yet undetermined conformational or electrostatic differences between the co I and co II states of MPO, which are absent in HRP.

Published
2006

225. Quantitative analysis of substrate specificity of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26

Author

Kmunicek, Jan, Hynkova, Kamila, Jedlicka, Tomas, Nagata, Yuji, Negri, Ana, Gago, Federico, Wade, Rebecca C., and Damborsky, Jiri

Subjects
Alkanes -- Chemical properties, Alkanes -- Research, Chemistry, Analytic -- Quantitative, Chemistry, Analytic -- Research, Biological sciences, Chemistry
Abstract

The classical quantitative structure-activity relationship (QSAR) technique and comparative binding energy (COMBINE) analysis is simultaneously applied to analyze substrate specificity in the haloalkene dehalogenase LinB enzyme from Sphingomonas paucimobilis UT26. The mechanism of molecular adaptation toward a different specificity is discussed on the basis of quantitative comparison of models derived for two protein family members.

Published
2005

226. Exploiting the 2-Amino-1,3,4-thiadiazole Scaffold To Inhibit Trypanosoma brucei Pteridine Reductase in Support of Early-Stage Drug Discovery

Author

Linciano, Pasquale, primary, Dawson, Alice, additional, Pöhner, Ina, additional, Costa, David M., additional, Sá, Monica S., additional, Cordeiro-da-Silva, Anabela, additional, Luciani, Rosaria, additional, Gul, Sheraz, additional, Witt, Gesa, additional, Ellinger, Bernhard, additional, Kuzikov, Maria, additional, Gribbon, Philip, additional, Reinshagen, Jeanette, additional, Wolf, Markus, additional, Behrens, Birte, additional, Hannaert, Véronique, additional, Michels, Paul A. M., additional, Nerini, Erika, additional, Pozzi, Cecilia, additional, di Pisa, Flavio, additional, Landi, Giacomo, additional, Santarem, Nuno, additional, Ferrari, Stefania, additional, Saxena, Puneet, additional, Lazzari, Sandra, additional, Cannazza, Giuseppe, additional, Freitas-Junior, Lucio H., additional, Moraes, Carolina B., additional, Pascoalino, Bruno S., additional, Alcântara, Laura M., additional, Bertolacini, Claudia P., additional, Fontana, Vanessa, additional, Wittig, Ulrike, additional, Müller, Wolfgang, additional, Wade, Rebecca C., additional, Hunter, William N., additional, Mangani, Stefano, additional, Costantino, Luca, additional, and Costi, Maria P., additional

Published
2017
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228. Kinetics for Drug Discovery: an industry-driven effort to target drug residence time

Author

Schuetz, Doris A., primary, de Witte, Wilhelmus Egbertus Arnout, additional, Wong, Yin Cheong, additional, Knasmueller, Bernhard, additional, Richter, Lars, additional, Kokh, Daria B., additional, Sadiq, S. Kashif, additional, Bosma, Reggie, additional, Nederpelt, Indira, additional, Heitman, Laura H., additional, Segala, Elena, additional, Amaral, Marta, additional, Guo, Dong, additional, Andres, Dorothee, additional, Georgi, Victoria, additional, Stoddart, Leigh A., additional, Hill, Steve, additional, Cooke, Robert M., additional, De Graaf, Chris, additional, Leurs, Rob, additional, Frech, Matthias, additional, Wade, Rebecca C., additional, de Lange, Elizabeth Cunera Maria, additional, IJzerman, Adriaan P., additional, Müller-Fahrnow, Anke, additional, and Ecker, Gerhard F., additional

Published
2017
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229. A unique profilin-actin interface is important for malaria parasite motility

Author

Moreau, Catherine A., primary, Bhargav, Saligram P., additional, Kumar, Hirdesh, additional, Quadt, Katharina A., additional, Piirainen, Henni, additional, Strauss, Léanne, additional, Kehrer, Jessica, additional, Streichfuss, Martin, additional, Spatz, Joachim P., additional, Wade, Rebecca C., additional, Kursula, Inari, additional, and Frischknecht, Friedrich, additional

Published
2017
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233. Chroman-4-One Derivatives Targeting Pteridine Reductase 1 and Showing Anti-Parasitic Activity

Author

Di Pisa, Flavio, primary, Landi, Giacomo, additional, Dello Iacono, Lucia, additional, Pozzi, Cecilia, additional, Borsari, Chiara, additional, Ferrari, Stefania, additional, Santucci, Matteo, additional, Santarem, Nuno, additional, Cordeiro-da-Silva, Anabela, additional, Moraes, Carolina, additional, Alcantara, Laura, additional, Fontana, Vanessa, additional, Freitas-Junior, Lucio, additional, Gul, Sheraz, additional, Kuzikov, Maria, additional, Behrens, Birte, additional, Pöhner, Ina, additional, Wade, Rebecca, additional, Costi, Maria, additional, and Mangani, Stefano, additional

Published
2017
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234. Dynamics of CYP51: implications for function and inhibitor design

Author

Yu, Xiaofeng, Cojocaru, Vlad, Mustafa, Ghulam, Salo-Ahen, Outi M. H., Lepesheva, Galina I., and Wade, Rebecca C.

Subjects
Trypanosoma brucei brucei, Protozoan Proteins, Hydrogen Bonding, Molecular Dynamics Simulation, Crystallography, X-Ray, Article, Protein Structure, Secondary, Substrate Specificity, Sterol 14-Demethylase, Catalytic Domain, Drug Design, Solvents, Humans, Cytochrome P-450 CYP2C9
Abstract

Sterol 14α-demethylase (cytochrome P450 family 51 (CYP51)) is an essential enzyme occurring in all biological kingdoms. In eukaryotes, it is located in the membrane of the endoplasmic reticulum. Selective inhibitors of trypanosomal CYP51s that do not affect the human CYP51 have been discovered in vitro and found to cure acute and chronic mouse Chagas disease without severe side effects in vivo. Crystal structures indicate that CYP51 may be more rigid than most CYPs, and it has been proposed that this property may facilitate antiparasitic drug design. Therefore, to investigate the dynamics of trypanosomal CYP51, we built a model of membrane-bound Trypanosoma brucei CYP51 and then performed molecular dynamics simulations of T. brucei CYP51 in membrane-bound and soluble forms. We compared the dynamics of T. brucei CYP51 with those of human CYP51, CYP2C9, and CYP2E1. In the simulations, the CYP51s display low mobility in the buried active site although overall mobility is similar in all the CYPs studied. The simulations suggest that in CYP51, pathway 2f serves as the major ligand access tunnel, and both pathways 2f (leading to membrane) and S (leading to solvent) can serve as ligand egress tunnels. Compared with the other CYPs, the residues at the entrance of the ligand access tunnels in CYP51 have higher mobility that may be necessary to facilitate the passage of its large sterol ligands. The water (W) tunnel is accessible to solvent during most of the simulations of CYP51, but its width is affected by the conformations of the heme's two propionate groups. These differ from those observed in the other CYPs studied because of differences in their hydrogen-bonding network. Our simulations give insights into the dynamics of CYP51 that complement the available experimental data and have implications for drug design against CYP51 enzymes.

Published
2015

236. A community effort in SARS‐CoV‐2 drug discovery

Author

Schimunek, Johannes, Seidl, Philipp, Elez, Katarina, Hempel, Tim, Le, Tuan, Noé, Frank, Olsson, Simon, Raich, Lluís, Winter, Robin, Gokcan, Hatice, Gusev, Filipp, Gutkin, Evgeny M., Isayev, Olexandr, Kurnikova, Maria G., Narangoda, Chamali H., Zubatyuk, Roman, Bosko, Ivan P., Furs, Konstantin V., Karpenko, Anna D., Kornoushenko, Yury V., Shuldau, Mikita, Yushkevich, Artsemi, Benabderrahmane, Mohammed B., Bousquet‐Melou, Patrick, Bureau, Ronan, Charton, Beatrice, Cirou, Bertrand C., Gil, Gérard, Allen, William J., Sirimulla, Suman, Watowich, Stanley, Antonopoulos, Nick, Epitropakis, Nikolaos, Krasoulis, Agamemnon, Itsikalis, Vassilis, Theodorakis, Stavros, Kozlovskii, Igor, Maliutin, Anton, Medvedev, Alexander, Popov, Petr, Zaretckii, Mark, Eghbal‐Zadeh, Hamid, Halmich, Christina, Hochreiter, Sepp, Mayr, Andreas, Ruch, Peter, Widrich, Michael, Berenger, Francois, Kumar, Ashutosh, Yamanishi, Yoshihiro, Zhang, Kam Y. J., Bengio, Emmanuel, Bengio, Yoshua, Jain, Moksh J., Korablyov, Maksym, Liu, Cheng‐Hao, Marcou, Gilles, Glaab, Enrico, Barnsley, Kelly, Iyengar, Suhasini M., Ondrechen, Mary Jo, Haupt, V. Joachim, Kaiser, Florian, Schroeder, Michael, Pugliese, Luisa, Albani, Simone, Athanasiou, Christina, Beccari, Andrea, Carloni, Paolo, D'Arrigo, Giulia, Gianquinto, Eleonora, Goßen, Jonas, Hanke, Anton, Joseph, Benjamin P., Kokh, Daria B., Kovachka, Sandra, Manelfi, Candida, Mukherjee, Goutam, Muñiz‐Chicharro, Abraham, Musiani, Francesco, Nunes‐Alves, Ariane, Paiardi, Giulia, Rossetti, Giulia, Sadiq, S. Kashif, Spyrakis, Francesca, Talarico, Carmine, Tsengenes, Alexandros, Wade, Rebecca C., Copeland, Conner, Gaiser, Jeremiah, Olson, Daniel R., Roy, Amitava, Venkatraman, Vishwesh, Wheeler, Travis J., Arthanari, Haribabu, Blaschitz, Klara, Cespugli, Marco, Durmaz, Vedat, Fackeldey, Konstantin, Fischer, Patrick D., Gorgulla, Christoph, Gruber, Christian, Gruber, Karl, Hetmann, Michael, Kinney, Jamie E., Padmanabha Das, Krishna M., Pandita, Shreya, Singh, Amit, Steinkellner, Georg, Tesseyre, Guilhem, Wagner, Gerhard, Wang, Zi‐Fu, Yust, Ryan J., Druzhilovskiy, Dmitry S., Filimonov, Dmitry A., Pogodin, Pavel V., Poroikov, Vladimir, Rudik, Anastassia V., Stolbov, Leonid A., Veselovsky, Alexander V., De Rosa, Maria, De Simone, Giada, Gulotta, Maria R., Lombino, Jessica, Mekni, Nedra, Perricone, Ugo, Casini, Arturo, Embree, Amanda, Gordon, D. Benjamin, Lei, David, Pratt, Katelin, Voigt, Christopher A., Chen, Kuang‐Yu, Jacob, Yves, Krischuns, Tim, Lafaye, Pierre, Zettor, Agnès, Rodríguez, M. Luis, White, Kris M., Fearon, Daren, Von Delft, Frank, Walsh, Martin A., Horvath, Dragos, Brooks, Charles L., Falsafi, Babak, Ford, Bryan, García‐Sastre, Adolfo, Yup Lee, Sang, Naffakh, Nadia, Varnek, Alexandre, Klambauer, Günter, and Hermans, Thomas M.

Abstract

The COVID‐19 pandemic continues to pose a substantial threat to human lives and is likely to do so for years to come. Despite the availability of vaccines, searching for efficient small‐molecule drugs that are widely available, including in low‐ and middle‐income countries, is an ongoing challenge. In this work, we report the results of an open science community effort, the “Billion molecules against COVID‐19 challenge”, to identify small‐molecule inhibitors against SARS‐CoV‐2 or relevant human receptors. Participating teams used a wide variety of computational methods to screen a minimum of 1 billion virtual molecules against 6 protein targets. Overall, 31 teams participated, and they suggested a total of 639,024 molecules, which were subsequently ranked to find ‘consensus compounds’. The organizing team coordinated with various contract research organizations (CROs) and collaborating institutions to synthesize and test 878 compounds for biological activity against proteases (Nsp5, Nsp3, TMPRSS2), nucleocapsid N, RdRP (only the Nsp12 domain), and (alpha) spike protein S. Overall, 27 compounds with weak inhibition/binding were experimentally identified by binding‐, cleavage‐, and/or viral suppression assays and are presented here. Open science approaches such as the one presented here contribute to the knowledge base of future drug discovery efforts in finding better SARS‐CoV‐2 treatments.

Published
2024
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237. Global profiling of SRP interaction with nascent polypeptides

Author

Schibich, Daniela, Gloge, Felix, Poehner, Ina, Björkholm, Patrik, Wade, Rebecca C., von Heijne, Gunnar, Bukau, Bernd, Kramer, Guenter, Schibich, Daniela, Gloge, Felix, Poehner, Ina, Björkholm, Patrik, Wade, Rebecca C., von Heijne, Gunnar, Bukau, Bernd, and Kramer, Guenter

Abstract

Signal recognition particle (SRP) is a universally conserved protein-RNA complex that mediates co-translational protein translocation and membrane insertion by targeting translating ribosomes to membrane translocons(1). The existence of parallel co- and post-translational transport pathways(2), however, raises the question of the cellular substrate pool of SRP and the molecular basis of substrate selection. Here we determine the binding sites of bacterial SRP within the nascent proteome of Escherichia coli at amino acid resolution, by sequencing messenger RNA footprints of ribosome-nascent-chain complexes associated with SRP. SRP, on the basis of its strong preference for hydrophobic transmembrane domains (TMDs), constitutes a compartment-specific targeting factor for nascent inner membrane proteins (IMPs) that efficiently excludes signal-sequence-containing precursors of periplasmic and outer membrane proteins. SRP associates with hydrophobic TMDs enriched in consecutive stretches of hydrophobic and bulky aromatic amino acids immediately on their emergence from the ribosomal exit tunnel. By contrast with current models, N-terminal TMDs are frequently skipped and TMDs internal to the polypeptide sequence are selectively recognized. Furthermore, SRP binds several TMDs in many multi-spanning membrane proteins, suggesting cycles of SRP-mediated membrane targeting. SRP-mediated targeting is not accompanied by a transient slowdown of translation and is not influenced by the ribosome-associated chaperone trigger factor (TF), which has a distinct substrate pool and acts at different stages during translation. Overall, our proteome-wide data set of SRP-binding sites reveals the underlying principles of pathway decisions for nascent chains in bacteria, with SRP acting as the dominant triaging factor, sufficient to separate IMPs from substrates of the SecA-SecB post-translational translocation and TF-assisted cytosolic protein folding pathways.

Published
2016
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238. Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

Author

NMR Spectroscopy, Sub NMR Spectroscopy, Lensink, Marc F., Velankar, Sameer, Kryshtafovych, Andriy, Huang, Shen You, Schneidman-Duhovny, Dina, Sali, Andrej, Segura, Joan, Fernandez-Fuentes, Narcis, Viswanath, Shruthi, Elber, Ron, Grudinin, Sergei, Popov, Petr, Neveu, Emilie, Lee, Hasup, Baek, Minkyung, Park, Sangwoo, Heo, Lim, Rie Lee, Gyu, Seok, Chaok, Qin, Sanbo, Zhou, Huan Xiang, Ritchie, David W., Maigret, Bernard, Devignes, Marie Dominique, Ghoorah, Anisah, Torchala, Mieczyslaw, Chaleil, Raphaël A G, Bates, Paul A., Ben-Zeev, Efrat, Eisenstein, Miriam, Negi, Surendra S., Weng, Zhiping, Vreven, Thom, Pierce, Brian G., Borrman, Tyler M., Yu, Jinchao, Ochsenbein, Françoise, Guerois, Raphaël, Vangone, Anna, Garcia Lopes Maia Rodrigues, João, van Zundert, Gydo, Nellen, Mehdi, Xue, Li, Karaca, Ezgi, Melquiond, Adrien S J, Visscher, Koen, Kastritis, Panagiotis L., Bonvin, Alexandre M J J, Xu, Xianjin, Qiu, Liming, Yan, Chengfei, Li, Jilong, Ma, Zhiwei, Cheng, Jianlin, Zou, Xiaoqin, Shen, Yang, Peterson, Lenna X., Kim, Hyung Rae, Roy, Amit, Han, Xusi, Esquivel-Rodriguez, Juan, Kihara, Daisuke, Yu, Xiaofeng, Bruce, Neil J., Fuller, Jonathan C., Wade, Rebecca C., Anishchenko, Ivan, Kundrotas, Petras J., Vakser, Ilya A., Imai, Kenichiro, Yamada, Kazunori, Oda, Toshiyuki, Nakamura, Tsukasa, Tomii, Kentaro, Pallara, Chiara, Romero-Durana, Miguel, Jiménez-García, Brian, Moal, Iain H., Férnandez-Recio, Juan, Joung, Jong Young, Kim, Jong Yun, Joo, Keehyoung, Lee, Jooyoung, Kozakov, Dima, Vajda, Sandor, Mottarella, Scott, Hall, David R., Beglov, Dmitri, Mamonov, Artem, Xia, Bing, Bohnuud, Tanggis, Del Carpio, Carlos A., Ichiishi, Eichiro, Marze, Nicholas, Kuroda, Daisuke, Roy Burman, Shourya S., Gray, Jeffrey J., Chermak, Edrisse, Cavallo, Luigi, Oliva, Romina, Tovchigrechko, Andrey, Wodak, Shoshana J., NMR Spectroscopy, Sub NMR Spectroscopy, Lensink, Marc F., Velankar, Sameer, Kryshtafovych, Andriy, Huang, Shen You, Schneidman-Duhovny, Dina, Sali, Andrej, Segura, Joan, Fernandez-Fuentes, Narcis, Viswanath, Shruthi, Elber, Ron, Grudinin, Sergei, Popov, Petr, Neveu, Emilie, Lee, Hasup, Baek, Minkyung, Park, Sangwoo, Heo, Lim, Rie Lee, Gyu, Seok, Chaok, Qin, Sanbo, Zhou, Huan Xiang, Ritchie, David W., Maigret, Bernard, Devignes, Marie Dominique, Ghoorah, Anisah, Torchala, Mieczyslaw, Chaleil, Raphaël A G, Bates, Paul A., Ben-Zeev, Efrat, Eisenstein, Miriam, Negi, Surendra S., Weng, Zhiping, Vreven, Thom, Pierce, Brian G., Borrman, Tyler M., Yu, Jinchao, Ochsenbein, Françoise, Guerois, Raphaël, Vangone, Anna, Garcia Lopes Maia Rodrigues, João, van Zundert, Gydo, Nellen, Mehdi, Xue, Li, Karaca, Ezgi, Melquiond, Adrien S J, Visscher, Koen, Kastritis, Panagiotis L., Bonvin, Alexandre M J J, Xu, Xianjin, Qiu, Liming, Yan, Chengfei, Li, Jilong, Ma, Zhiwei, Cheng, Jianlin, Zou, Xiaoqin, Shen, Yang, Peterson, Lenna X., Kim, Hyung Rae, Roy, Amit, Han, Xusi, Esquivel-Rodriguez, Juan, Kihara, Daisuke, Yu, Xiaofeng, Bruce, Neil J., Fuller, Jonathan C., Wade, Rebecca C., Anishchenko, Ivan, Kundrotas, Petras J., Vakser, Ilya A., Imai, Kenichiro, Yamada, Kazunori, Oda, Toshiyuki, Nakamura, Tsukasa, Tomii, Kentaro, Pallara, Chiara, Romero-Durana, Miguel, Jiménez-García, Brian, Moal, Iain H., Férnandez-Recio, Juan, Joung, Jong Young, Kim, Jong Yun, Joo, Keehyoung, Lee, Jooyoung, Kozakov, Dima, Vajda, Sandor, Mottarella, Scott, Hall, David R., Beglov, Dmitri, Mamonov, Artem, Xia, Bing, Bohnuud, Tanggis, Del Carpio, Carlos A., Ichiishi, Eichiro, Marze, Nicholas, Kuroda, Daisuke, Roy Burman, Shourya S., Gray, Jeffrey J., Chermak, Edrisse, Cavallo, Luigi, Oliva, Romina, Tovchigrechko, Andrey, and Wodak, Shoshana J.

Published
2016

239. Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.

Author

Lensink, Marc, Lensink, Marc, Velankar, Sameer, Kryshtafovych, Andriy, Huang, Shen-You, Schneidman-Duhovny, Dina, Sali, Andrej, Segura, Joan, Fernandez-Fuentes, Narcis, Viswanath, Shruthi, Elber, Ron, Grudinin, Sergei, Popov, Petr, Neveu, Emilie, Lee, Hasup, Baek, Minkyung, Park, Sangwoo, Heo, Lim, Rie Lee, Gyu, Seok, Chaok, Qin, Sanbo, Zhou, Huan-Xiang, Ritchie, David, Maigret, Bernard, Devignes, Marie-Dominique, Ghoorah, Anisah, Torchala, Mieczyslaw, Chaleil, Raphaël, Bates, Paul, Ben-Zeev, Efrat, Eisenstein, Miriam, Negi, Surendra, Weng, Zhiping, Vreven, Thom, Pierce, Brian, Borrman, Tyler, Yu, Jinchao, Ochsenbein, Françoise, Guerois, Raphaël, Vangone, Anna, Rodrigues, João, van Zundert, Gydo, Nellen, Mehdi, Xue, Li, Karaca, Ezgi, Melquiond, Adrien, Visscher, Koen, Kastritis, Panagiotis, Bonvin, Alexandre, Xu, Xianjin, Qiu, Liming, Yan, Chengfei, Li, Jilong, Ma, Zhiwei, Cheng, Jianlin, Zou, Xiaoqin, Shen, Yang, Peterson, Lenna, Kim, Hyung-Rae, Roy, Amit, Han, Xusi, Esquivel-Rodriguez, Juan, Kihara, Daisuke, Yu, Xiaofeng, Bruce, Neil, Fuller, Jonathan, Wade, Rebecca, Anishchenko, Ivan, Kundrotas, Petras, Vakser, Ilya, Imai, Kenichiro, Yamada, Kazunori, Oda, Toshiyuki, Nakamura, Tsukasa, Tomii, Kentaro, Pallara, Chiara, Romero-Durana, Miguel, Jiménez-García, Brian, Moal, Iain, Férnandez-Recio, Juan, Joung, Jong, Kim, Jong, Joo, Keehyoung, Lee, Jooyoung, Kozakov, Dima, Vajda, Sandor, Mottarella, Scott, Hall, David, Beglov, Dmitri, Mamonov, Artem, Xia, Bing, Bohnuud, Tanggis, Del Carpio, Carlos, Ichiishi, Eichiro, Marze, Nicholas, Kuroda, Daisuke, Roy Burman, Shourya, Gray, Jeffrey, Chermak, Edrisse, Cavallo, Luigi, Lensink, Marc, Lensink, Marc, Velankar, Sameer, Kryshtafovych, Andriy, Huang, Shen-You, Schneidman-Duhovny, Dina, Sali, Andrej, Segura, Joan, Fernandez-Fuentes, Narcis, Viswanath, Shruthi, Elber, Ron, Grudinin, Sergei, Popov, Petr, Neveu, Emilie, Lee, Hasup, Baek, Minkyung, Park, Sangwoo, Heo, Lim, Rie Lee, Gyu, Seok, Chaok, Qin, Sanbo, Zhou, Huan-Xiang, Ritchie, David, Maigret, Bernard, Devignes, Marie-Dominique, Ghoorah, Anisah, Torchala, Mieczyslaw, Chaleil, Raphaël, Bates, Paul, Ben-Zeev, Efrat, Eisenstein, Miriam, Negi, Surendra, Weng, Zhiping, Vreven, Thom, Pierce, Brian, Borrman, Tyler, Yu, Jinchao, Ochsenbein, Françoise, Guerois, Raphaël, Vangone, Anna, Rodrigues, João, van Zundert, Gydo, Nellen, Mehdi, Xue, Li, Karaca, Ezgi, Melquiond, Adrien, Visscher, Koen, Kastritis, Panagiotis, Bonvin, Alexandre, Xu, Xianjin, Qiu, Liming, Yan, Chengfei, Li, Jilong, Ma, Zhiwei, Cheng, Jianlin, Zou, Xiaoqin, Shen, Yang, Peterson, Lenna, Kim, Hyung-Rae, Roy, Amit, Han, Xusi, Esquivel-Rodriguez, Juan, Kihara, Daisuke, Yu, Xiaofeng, Bruce, Neil, Fuller, Jonathan, Wade, Rebecca, Anishchenko, Ivan, Kundrotas, Petras, Vakser, Ilya, Imai, Kenichiro, Yamada, Kazunori, Oda, Toshiyuki, Nakamura, Tsukasa, Tomii, Kentaro, Pallara, Chiara, Romero-Durana, Miguel, Jiménez-García, Brian, Moal, Iain, Férnandez-Recio, Juan, Joung, Jong, Kim, Jong, Joo, Keehyoung, Lee, Jooyoung, Kozakov, Dima, Vajda, Sandor, Mottarella, Scott, Hall, David, Beglov, Dmitri, Mamonov, Artem, Xia, Bing, Bohnuud, Tanggis, Del Carpio, Carlos, Ichiishi, Eichiro, Marze, Nicholas, Kuroda, Daisuke, Roy Burman, Shourya, Gray, Jeffrey, Chermak, Edrisse, and Cavallo, Luigi

Abstract

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.

Published
2016

240. Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

Author

Barcelona Supercomputing Center, Lesink, Marc F., Velankar, Sameer, Kryshtafovych, Andriy, Huang, Shen-You, Schneidman-Duhovny, Dina, Sali, Andrej, Segura, Joan, Fernandez-Fuentes, Narcis, Shruthi, Viswanath, Elber, Ron, Grudinin, Sergei, Popov, Petr, Neveu, Emilie, Lee, Hasup, Baek, Minkyung, Park, Sangwoo, Heo, Lim, Lee, Gyu R., Seok, Chaok, Qin, Sanbo, Zhou, Huan-Xiang, Ritchie, David W., Maigret, Bernard, Devignes, Marie-Dominique, Ghoorah, Anisah, Torchala, Mieczyslaw, Chaleil, Raphaël A.G., Bates, Paul A., Ben-Zeev, Efrat, Eisenstein, Miriam, Negi, Surendra S., Weng, Zhiping, Vreven, Thom, Pierce, Brian G., Borrman, Tyler M., Yu, Jinchao, Ochsenbein, Françoise, Guerois, Raphaël, Vangone, Anna, Rodrigues, Joao P.G.L.M., Zundert, Gydo van, Nellen, Mehdi, Xue, Li, Karaca, Ezgi, Melquiond, Adrien S.J., Visscher, Koen, Kastritis, Panagiotis L., Bonvin, Alexandre M.J.J., Xianjin, Xu, Qiu, Liming, Yan, Chengfei, Li, Jilong, Ma, Zhiwei, Cheng, Jianlin, Zou, Xiaoqin, Shen, Yang, Peterson, Lenna X., Kim, Hyung-Rae, Roy, Amit, Han, Xusi, Esquivel-Rodriguez, Juan, Kihara, Daisuke, Yu, Xiaofeng, Bruce, Neil J., Fuller, Jonathan C., Wade, Rebecca C., Anishchenko, Ivan, Kundrotas, Petras J., Vakser, Ilya A., Imai, Kenichiro, Yamada, Kazunori, Oda, Toshiyuki, Nakamura, Tsukasa, Tomii, Kentaro, Pallara, Chiara, Romero-Durana, Miguel, Jiménez-García, Brian, Moal, Iain H., Fernández-Recio, Juan, Joung, Jong Y., Kim, Jong Y., Joo, Keehyoung, Lee, Jooyoung, Kozakov, Dima, Vajda, Sandor, Mottarella, Scott, Hall, David R., Beglov, Dmitri, Mamonov, Artem, Xia, Bing, Bohnuud, Tanggis, del Carpio, Carlos A., Ichiishi, Eichiro, Marze, Nicholas, Kuroda, Daisuke, Burman, Shourya S., Gray, Jeffrey J., Chermak, Edrisse, Cavallo, Luigi, Oliva, Romina, Tovchigrechko, Andrey, Wodak, Shoshana J., Barcelona Supercomputing Center, Lesink, Marc F., Velankar, Sameer, Kryshtafovych, Andriy, Huang, Shen-You, Schneidman-Duhovny, Dina, Sali, Andrej, Segura, Joan, Fernandez-Fuentes, Narcis, Shruthi, Viswanath, Elber, Ron, Grudinin, Sergei, Popov, Petr, Neveu, Emilie, Lee, Hasup, Baek, Minkyung, Park, Sangwoo, Heo, Lim, Lee, Gyu R., Seok, Chaok, Qin, Sanbo, Zhou, Huan-Xiang, Ritchie, David W., Maigret, Bernard, Devignes, Marie-Dominique, Ghoorah, Anisah, Torchala, Mieczyslaw, Chaleil, Raphaël A.G., Bates, Paul A., Ben-Zeev, Efrat, Eisenstein, Miriam, Negi, Surendra S., Weng, Zhiping, Vreven, Thom, Pierce, Brian G., Borrman, Tyler M., Yu, Jinchao, Ochsenbein, Françoise, Guerois, Raphaël, Vangone, Anna, Rodrigues, Joao P.G.L.M., Zundert, Gydo van, Nellen, Mehdi, Xue, Li, Karaca, Ezgi, Melquiond, Adrien S.J., Visscher, Koen, Kastritis, Panagiotis L., Bonvin, Alexandre M.J.J., Xianjin, Xu, Qiu, Liming, Yan, Chengfei, Li, Jilong, Ma, Zhiwei, Cheng, Jianlin, Zou, Xiaoqin, Shen, Yang, Peterson, Lenna X., Kim, Hyung-Rae, Roy, Amit, Han, Xusi, Esquivel-Rodriguez, Juan, Kihara, Daisuke, Yu, Xiaofeng, Bruce, Neil J., Fuller, Jonathan C., Wade, Rebecca C., Anishchenko, Ivan, Kundrotas, Petras J., Vakser, Ilya A., Imai, Kenichiro, Yamada, Kazunori, Oda, Toshiyuki, Nakamura, Tsukasa, Tomii, Kentaro, Pallara, Chiara, Romero-Durana, Miguel, Jiménez-García, Brian, Moal, Iain H., Fernández-Recio, Juan, Joung, Jong Y., Kim, Jong Y., Joo, Keehyoung, Lee, Jooyoung, Kozakov, Dima, Vajda, Sandor, Mottarella, Scott, Hall, David R., Beglov, Dmitri, Mamonov, Artem, Xia, Bing, Bohnuud, Tanggis, del Carpio, Carlos A., Ichiishi, Eichiro, Marze, Nicholas, Kuroda, Daisuke, Burman, Shourya S., Gray, Jeffrey J., Chermak, Edrisse, Cavallo, Luigi, Oliva, Romina, Tovchigrechko, Andrey, and Wodak, Shoshana J.

Abstract

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., We are most grateful to the PDBe at the European Bioinformatics Institute in Hinxton, UK, for hosting the CAPRI website. Our deepest thanks go to all the structural biologists and to the following structural genomics initiatives: Northeast Structural Genomics Consortium, Joint Center for Structural Genomics, NatPro PSI:Biology, New York Structural Genomics Research Center, Midwest Center for Structural Genomics, Structural Genomics Consortium, for contributing the targets for this joint CASP-CAPRI experiment. MFL acknowledges support from the FRABio FR3688 Research Federation “Structural & Functional Biochemistry of Biomolecular Assemblies.”, Peer Reviewed, Postprint (published version)

Published
2016

246. Profiling of Flavonol Derivatives for the Development of Antitrypanosomatidic Drugs

Author

Borsari, Chiara, primary, Luciani, Rosaria, additional, Pozzi, Cecilia, additional, Poehner, Ina, additional, Henrich, Stefan, additional, Trande, Matteo, additional, Cordeiro-da-Silva, Anabela, additional, Santarem, Nuno, additional, Baptista, Catarina, additional, Tait, Annalisa, additional, Di Pisa, Flavio, additional, Dello Iacono, Lucia, additional, Landi, Giacomo, additional, Gul, Sheraz, additional, Wolf, Markus, additional, Kuzikov, Maria, additional, Ellinger, Bernhard, additional, Reinshagen, Jeanette, additional, Witt, Gesa, additional, Gribbon, Philip, additional, Kohler, Manfred, additional, Keminer, Oliver, additional, Behrens, Birte, additional, Costantino, Luca, additional, Tejera Nevado, Paloma, additional, Bifeld, Eugenia, additional, Eick, Julia, additional, Clos, Joachim, additional, Torrado, Juan, additional, Jiménez-Antón, María D., additional, Corral, María J., additional, Alunda, José M, additional, Pellati, Federica, additional, Wade, Rebecca C., additional, Ferrari, Stefania, additional, Mangani, Stefano, additional, and Costi, Maria Paola, additional

Published
2016
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