29 results on '"Stefan Bietz"'
Search Results
2. ProteinsPlus: a web portal for structure analysis of macromolecules.
- Author
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Rainer Fährrolfes, Stefan Bietz, Florian Flachsenberg, Agnes Meyder, Eva Nittinger, Thomas Otto, Andrea Volkamer, and Matthias Rarey
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- 2017
- Full Text
- View/download PDF
3. Index-Based Searching of Interaction Patterns in Large Collections of Protein-Ligand Interfaces.
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Therese Inhester, Stefan Bietz, Matthias Hilbig 0001, Robert Schmidt 0002, and Matthias Rarey
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- 2017
- Full Text
- View/download PDF
4. NAOMInova: Interactive Geometric Analysis of Noncovalent Interactions in Macromolecular Structures.
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Therese Inhester, Eva Nittinger, Kai Sommer, Pascal Schmidt, Stefan Bietz, and Matthias Rarey
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- 2017
- Full Text
- View/download PDF
5. mRAISE: an alternative algorithmic approach to ligand-based virtual screening.
- Author
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Mathias M. von Behren, Stefan Bietz, Eva Nittinger, and Matthias Rarey
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- 2016
- Full Text
- View/download PDF
6. UNICON: A Powerful and Easy-to-Use Compound Library Converter.
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Kai Sommer, Nils-Ole Friedrich, Stefan Bietz, Matthias Hilbig 0001, Therese Inhester, and Matthias Rarey
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- 2016
- Full Text
- View/download PDF
7. SIENA: Efficient Compilation of Selective Protein Binding Site Ensembles.
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Stefan Bietz and Matthias Rarey
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- 2016
- Full Text
- View/download PDF
8. Discriminative Chemical Patterns: Automatic and Interactive Design.
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Stefan Bietz, Karen T. Schomburg, Matthias Hilbig 0001, and Matthias Rarey
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- 2015
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- View/download PDF
9. ASCONA: Rapid Detection and Alignment of Protein Binding Site Conformations.
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Stefan Bietz and Matthias Rarey
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- 2015
- Full Text
- View/download PDF
10. Facing the Challenges of Structure-Based Target Prediction by Inverse Virtual Screening.
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Karen Schomburg, Stefan Bietz, Hans Briem, Angela M. Henzler, Sascha Urbaczek, and Matthias Rarey
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- 2014
- Full Text
- View/download PDF
11. Placement of Water Molecules in Protein Structures: From Large-Scale Evaluations to Single-Case Examples
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Stefan Bietz, Robert Klein, Florian Flachsenberg, Matthias Rarey, Gudrun Lange, and Eva Nittinger
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Models, Molecular ,0301 basic medicine ,Binding Sites ,Protein Conformation ,Computer science ,General Chemical Engineering ,Scale (chemistry) ,Proteins ,Water ,General Chemistry ,Library and Information Sciences ,Ligands ,Computer Science Applications ,03 medical and health sciences ,030104 developmental biology ,Protein structure ,Thermodynamics ,Molecule ,Water chemistry ,Databases, Protein ,Representation (mathematics) ,Biological system ,Protein crystallization - Abstract
Water molecules are of great importance for the correct representation of ligand binding interactions. Throughout the last years, water molecules and their integration into drug design strategies have received increasing attention. Nowadays a variety of tools are available to place and score water molecules. However, the most frequently applied software solutions require substantial computational resources. In addition, none of the existing methods has been rigorously evaluated on the basis of a large number of diverse protein complexes. Therefore, we present a novel method for placing water molecules, called WarPP, based on interaction geometries previously derived from protein crystal structures. Using a large, previously compiled, high-quality validation set of almost 1500 protein-ligand complexes containing almost 20 000 crystallographically observed water molecules in their active sites, we validated our placement strategy. We correctly placed 80% of the water molecules within 1.0 Å of a crystallographically observed one.
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- 2018
12. From cheminformatics to structure-based design: Web services and desktop applications based on the NAOMI library
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Rainer Fährrolfes, Kai Sommer, Florian Flachsenberg, Mathias M. von Behren, Therese Inhester, Andrea Volkamer, Agnes Meyder, Thomas Otto, Eva Nittinger, Matthias Hilbig, Stefan Bietz, Florian Lauck, Matthias Rarey, and Karen T. Schomburg
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0301 basic medicine ,Computer science ,Druggability ,Bioengineering ,Bioinformatics ,computer.software_genre ,Applied Microbiology and Biotechnology ,03 medical and health sciences ,Structural bioinformatics ,Software ,Databases, Protein ,Internet ,Virtual screening ,business.industry ,Computational Biology ,General Medicine ,File format ,Visualization ,030104 developmental biology ,Cheminformatics ,Web service ,Software engineering ,business ,computer ,Biotechnology - Abstract
Nowadays, computational approaches are an integral part of life science research. Problems related to interpretation of experimental results, data analysis, or visualization tasks highly benefit from the achievements of the digital era. Simulation methods facilitate predictions of physicochemical properties and can assist in understanding macromolecular phenomena. Here, we will give an overview of the methods developed in our group that aim at supporting researchers from all life science areas. Based on state-of-the-art approaches from structural bioinformatics and cheminformatics, we provide software covering a wide range of research questions. Our all-in-one web service platform ProteinsPlus ( http://proteins.plus ) offers solutions for pocket and druggability prediction, hydrogen placement, structure quality assessment, ensemble generation, protein–protein interaction classification, and 2D-interaction visualization. Additionally, we provide a software package that contains tools targeting cheminformatics problems like file format conversion, molecule data set processing, SMARTS editing, fragment space enumeration, and ligand-based virtual screening. Furthermore, it also includes structural bioinformatics solutions for inverse screening, binding site alignment, and searching interaction patterns across structure libraries. The software package is available at http://software.zbh.uni-hamburg.de .
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- 2017
13. Protoss: a holistic approach to predict tautomers and protonation states in protein-ligand complexes.
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Stefan Bietz, Sascha Urbaczek, Benjamin Schulz, and Matthias Rarey
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- 2014
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14. Prediction of protein mutation effects based on dehydration and hydrogen bonding - A large-scale study
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Matthias Rarey, Robert Klein, Gudrun Lange, Nadine Schneider, Eva Nittinger, Stefan Bietz, Agnes Meyder, and Karen T. Schomburg
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0301 basic medicine ,Chemistry ,Hydrogen bond ,Point mutation ,Protein design ,Biochemistry ,Enzyme catalysis ,03 medical and health sciences ,030104 developmental biology ,Protein structure ,Directed mutagenesis ,Structural Biology ,Computational chemistry ,Mutation (genetic algorithm) ,Side chain ,Molecular Biology - Abstract
Reliable computational prediction of protein side chain conformations and the energetic impact of amino acid mutations are the key aspects for the optimization of biotechnologically relevant enzymatic reactions using structure-based design. By improving the protein stability, higher yields can be achieved. In addition, tuning the substrate selectivity of an enzymatic reaction by directed mutagenesis can lead to higher turnover rates. This work presents a novel approach to predict the conformation of a side chain mutation along with the energetic effect on the protein structure. The HYDE scoring concept applied here describes the molecular interactions primarily by evaluating the effect of dehydration and hydrogen bonding on molecular structures in aqueous solution. Here, we evaluate its capability of side-chain conformation prediction in classic remutation experiments. Furthermore, we present a new data set for evaluating "cross-mutations," a new experiment that resembles real-world application scenarios more closely. This data set consists of protein pairs with up to five point mutations. Thus, structural changes are attributed to point mutations only. In the cross-mutation experiment, the original protein structure is mutated with the aim to predict the structure of the side chain as in the paired mutated structure. The comparison of side chain conformation prediction ("remutation") showed that the performance of HYDEprotein is qualitatively comparable to state-of-the art methods. The ability of HYDEprotein to predict the energetic effect of a mutation is evaluated in the third experiment. Herein, the effect on protein stability is predicted correctly in 70% of the evaluated cases. Proteins 2017; 85:1550-1566. © 2017 Wiley Periodicals, Inc.
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- 2017
15. Large-Scale Analysis of Hydrogen Bond Interaction Patterns in Protein–Ligand Interfaces
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Gudrun Lange, Matthias Rarey, Agnes Meyder, Karen T. Schomburg, Therese Inhester, Robert Klein, Stefan Bietz, and Eva Nittinger
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0301 basic medicine ,Current (mathematics) ,Expected value ,Ligands ,010402 general chemistry ,01 natural sciences ,Molecular Docking Simulation ,03 medical and health sciences ,Protein structure ,Computational chemistry ,Drug Discovery ,Animals ,Humans ,Databases, Protein ,Computational model ,Basis (linear algebra) ,Hydrogen bond ,Chemistry ,Proteins ,Hydrogen Bonding ,0104 chemical sciences ,030104 developmental biology ,Chemical physics ,Molecular Medicine ,Protein ligand - Abstract
Protein-ligand interactions are the fundamental basis for molecular design in pharmaceutical research, biocatalysis, and agrochemical development. Especially hydrogen bonds are known to have special geometric requirements and therefore deserve a detailed analysis. In modeling approaches a more general description of hydrogen bond geometries, using distance and directionality, is applied. A first study of their geometries was performed based on 15 protein structures in 1982. Currently there are about 95 000 protein-ligand structures available in the PDB, providing a solid foundation for a new large-scale statistical analysis. Here, we report a comprehensive investigation of geometric and functional properties of hydrogen bonds. Out of 22 defined functional groups, eight are fully in accordance with theoretical predictions while 14 show variations from expected values. On the basis of these results, we derived interaction geometries to improve current computational models. It is expected that these observations will be useful in designing new chemical structures for biological applications.
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- 2017
16. Index-Based Searching of Interaction Patterns in Large Collections of Protein–Ligand Interfaces
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Robert Schmidt, Matthias Hilbig, Matthias Rarey, Stefan Bietz, and Therese Inhester
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Models, Molecular ,0301 basic medicine ,Time Factors ,Protein Conformation ,Computer science ,General Chemical Engineering ,Library and Information Sciences ,Ligands ,computer.software_genre ,Set (abstract data type) ,03 medical and health sciences ,Data Mining ,Structure (mathematical logic) ,Information retrieval ,Proteins ,General Chemistry ,Computer Science Applications ,ComputingMethodologies_PATTERNRECOGNITION ,030104 developmental biology ,Index (publishing) ,Key (cryptography) ,Design process ,Data mining ,computer ,Algorithms ,Protein Binding ,Protein ligand - Abstract
Comparison of three-dimensional interaction patterns in large collections of protein-ligand interfaces is a key element for understanding protein-ligand interactions and supports various steps in the structure-based drug design process. Different methods exist that provide query systems to search for geometrical patterns in protein-ligand complexes. However, these tools do not meet all of the requirements, which are high query variability, an adjustable search set, and high retrieval speed. Here we present a new tool named PELIKAN that is able to search for a variety of geometrical queries in large protein structure collections in a reasonably short time. The data are stored in an SQLite database that can easily be constructed from any set of protein-ligand complexes. We present different test queries demonstrating the performance of the PELIKAN approach. Furthermore, two application scenarios show the usefulness of PELIKAN in structure-based design endeavors.
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- 2017
17. Hydrogen placement in protein-ligand complexes under consideration of tautomerism.
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Stefan Bietz, Sascha Urbaczek, and Matthias Rarey
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- 2011
- Full Text
- View/download PDF
18. mRAISE: an alternative algorithmic approach to ligand-based virtual screening
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Stefan Bietz, Matthias Rarey, Mathias M. von Behren, and Eva Nittinger
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Models, Molecular ,0301 basic medicine ,Computer science ,Structural alignment ,Ligands ,computer.software_genre ,Machine learning ,03 medical and health sciences ,Search engine ,Drug Discovery ,Humans ,Physical and Theoretical Chemistry ,Databases, Protein ,Virtual screening ,Binding Sites ,business.industry ,Proteins ,computer.file_format ,Computer Science Applications ,030104 developmental biology ,Ranking ,Hit rate ,Bitmap ,Table (database) ,Pairwise comparison ,Data mining ,Artificial intelligence ,business ,computer ,Algorithms ,Databases, Chemical ,Software - Abstract
Ligand-based virtual screening is a well established method to find new lead molecules in todays drug discovery process. In order to be applicable in day to day practice, such methods have to face multiple challenges. The most important part is the reliability of the results, which can be shown and compared in retrospective studies. Furthermore, in the case of 3D methods, they need to provide biologically relevant molecular alignments of the ligands, that can be further investigated by a medicinal chemist. Last but not least, they have to be able to screen large databases in reasonable time. Many algorithms for ligand-based virtual screening have been proposed in the past, most of them based on pairwise comparisons. Here, a new method is introduced called mRAISE. Based on structural alignments, it uses a descriptor-based bitmap search engine (RAISE) to achieve efficiency. Alignments created on the fly by the search engine get evaluated with an independent shape-based scoring function also used for ranking of compounds. The correct ranking as well as the alignment quality of the method are evaluated and compared to other state of the art methods. On the commonly used Directory of Useful Decoys dataset mRAISE achieves an average area under the ROC curve of 0.76, an average enrichment factor at 1 % of 20.2 and an average hit rate at 1 % of 55.5. With these results, mRAISE is always among the top performing methods with available data for comparison. To access the quality of the alignments calculated by ligand-based virtual screening methods, we introduce a new dataset containing 180 prealigned ligands for 11 diverse targets. Within the top ten ranked conformations, the alignment closest to X-ray structure calculated with mRAISE has a root-mean-square deviation of less than 2.0 A for 80.8 % of alignment pairs and achieves a median of less than 2.0 A for eight of the 11 cases. The dataset used to rate the quality of the calculated alignments is freely available at http://www.zbh.uni-hamburg.de/mraise-dataset.html . The table of all PDB codes contained in the ensembles can be found in the supplementary material. The software tool mRAISE is freely available for evaluation purposes and academic use (see http://www.zbh.uni-hamburg.de/raise ).
- Published
- 2016
19. The Art of Compiling Protein Binding Site Ensembles
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Matthias Rarey, Stefan Bietz, and Rainer Fährrolfes
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0301 basic medicine ,Computer science ,Protein Data Bank (RCSB PDB) ,Plasma protein binding ,Computational biology ,Ligands ,computer.software_genre ,03 medical and health sciences ,Protein structure ,Structural Biology ,Drug Discovery ,Preprocessor ,Binding site ,Databases, Protein ,Binding Sites ,Organic Chemistry ,Proteins ,computer.file_format ,Protein Data Bank ,Computer Science Applications ,030104 developmental biology ,Fully automated ,Docking (molecular) ,Drug Design ,Molecular Medicine ,Data mining ,computer ,Software ,Protein Binding - Abstract
Structure-based drug design starts with the collection, preparation, and initial analysis of protein structures. With more than 115,000 structures publically available in the Protein Data Bank (PDB), fully automated processes reliably performing these important preprocessing steps are needed. Several tools are available for these tasks, however, most of them do not address the special needs of scientists interested in protein-ligand interactions. In this paper, we summarize our research activities towards an automated processing pipeline from raw PDB data towards ready-to-use protein binding site ensembles. Starting from a single protein structure, the pipeline covers the following phases: Extracting structurally related binding sites from the PDB, aligning disconnected binding site sequences, resolving tautomeric forms and protonation, orienting hydrogens and flippable side-chains, structurally aligning the multitude of binding sites, and performing a reasonable reduction of ensemble structures. The pipeline, named SIENA, creates protein-structural ensembles for the analysis of protein flexibility, molecular design efforts like docking or de novo design within seconds. For the first time, we are able to process the whole PDB in order to create a large collection of protein binding site ensembles. SIENA is available as part of the ZBH ProteinsPlus webserver under http://proteinsplus.zbh.uni-hamburg.de.
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- 2016
20. UNICON: A Powerful and Easy-to-Use Compound Library Converter
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Matthias Hilbig, Stefan Bietz, Matthias Rarey, Kai Sommer, Nils-Ole Friedrich, and Therese Inhester
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Models, Molecular ,0301 basic medicine ,Informatics ,Unicon ,Theoretical computer science ,Computer science ,General Chemical Engineering ,Molecular Conformation ,Library and Information Sciences ,computer.software_genre ,Small Molecule Libraries ,03 medical and health sciences ,Software ,Isomerism ,computer.programming_language ,Structure (mathematical logic) ,business.industry ,Programming language ,General Chemistry ,File format ,Computer Science Applications ,Task (computing) ,030104 developmental biology ,Workflow ,Cheminformatics ,Protons ,Line (text file) ,business ,computer - Abstract
The accurate handling of different chemical file formats and the consistent conversion between them play important roles for calculations in complex cheminformatics workflows. Working with different cheminformatic tools often makes the conversion between file formats a mandatory step. Such a conversion might become a difficult task in cases where the information content substantially differs. This paper describes UNICON, an easy-to-use software tool for this task. The functionality of UNICON ranges from file conversion between standard formats SDF, MOL2, SMILES, PDB, and PDBx/mmCIF via the generation of 2D structure coordinates and 3D structures to the enumeration of tautomeric forms, protonation states, and conformer ensembles. For this purpose, UNICON bundles the key elements of the previously described NAOMI library in a single, easy-to-use command line tool.
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- 2016
21. Prediction, Analysis, and Comparison of Active Sites
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Mathias M. von Behren, Matthias Rarey, Andrea Volkamer, and Stefan Bietz
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0301 basic medicine ,Protein structure database ,03 medical and health sciences ,030104 developmental biology ,010304 chemical physics ,Computer science ,0103 physical sciences ,Computational biology ,01 natural sciences - Published
- 2018
22. NAOMInova: Interactive Geometric Analysis of Noncovalent Interactions in Macromolecular Structures
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Stefan Bietz, Therese Inhester, Eva Nittinger, Matthias Rarey, Pascal Schmidt, and Kai Sommer
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0301 basic medicine ,Models, Molecular ,Geometric analysis ,Computer science ,Macromolecular Substances ,General Chemical Engineering ,Molecular Conformation ,Nanotechnology ,Library and Information Sciences ,01 natural sciences ,Set (abstract data type) ,03 medical and health sciences ,User-Computer Interface ,Protein structure ,Computer Graphics ,Non-covalent interactions ,chemistry.chemical_classification ,Computational Biology ,General Chemistry ,computer.file_format ,Protein Data Bank ,0104 chemical sciences ,Computer Science Applications ,010404 medicinal & biomolecular chemistry ,Variable (computer science) ,030104 developmental biology ,chemistry ,User interface ,Biological system ,computer ,Macromolecule - Abstract
Noncovalent interactions play an important role in macromolecular complexes. The assessment of molecular interactions is often based on knowledge derived from statistics on structural data. Within the last years, the available data in the Brookhaven Protein Data Bank has increased dramatically, quantitatively as well as qualitatively. This development allows the derivation of enhanced interaction models and motivates new ways of data analysis. Here, we present a method to facilitate the analysis of noncovalent interactions enabling detailed insights into the nature of molecular interactions. The method is integrated into a highly variable framework enabling the adaption to user-specific requirements. NAOMInova, the user interface for our method, allows the generation of specific statistics with respect to the chemical environment of substructures. The substructures as well as the analyzed set of protein structures can be chosen arbitrarily. Although NAOMInova was primarily made for data exploration in protein-ligand crystal structures, it can be used in combination with any structure collection, for example, analysis of a carbonyl in the neighborhood of an aromatic ring on a set of structures resulting from a MD simulation. Additionally, a filter for different atom attributes can be applied including the experimental support by electron density for single atoms. In this publication, we present the underlying algorithmic techniques of our method and show application examples that demonstrate NAOMInova's ability to support individual analysis of noncovalent interactions in protein structures. NAOMInova is available at http://www.zbh.uni-hamburg.de/naominova .
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- 2017
23. Corrigendum: The Art of Compiling Protein Binding Site Ensembles
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Rainer Fährrolfes, Matthias Rarey, and Stefan Bietz
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Crystallography ,Structural Biology ,Chemistry ,Organic Chemistry ,Drug Discovery ,Molecular Medicine ,Computational biology ,computer.file_format ,Plasma protein binding ,Protein Data Bank ,computer ,Computer Science Applications ,Protein ligand - Published
- 2017
24. Prediction of protein mutation effects based on dehydration and hydrogen bonding - A large-scale study
- Author
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Karen T, Schomburg, Eva, Nittinger, Agnes, Meyder, Stefan, Bietz, Nadine, Schneider, Gudrun, Lange, Robert, Klein, and Matthias, Rarey
- Subjects
Protein Conformation, alpha-Helical ,Protein Stability ,beta-Glucosidase ,Water ,Hydrogen Bonding ,Solutions ,Structure-Activity Relationship ,Amino Acid Substitution ,Humans ,Point Mutation ,Thermodynamics ,Protein Conformation, beta-Strand ,Amino Acids ,Desiccation ,Software - Abstract
Reliable computational prediction of protein side chain conformations and the energetic impact of amino acid mutations are the key aspects for the optimization of biotechnologically relevant enzymatic reactions using structure-based design. By improving the protein stability, higher yields can be achieved. In addition, tuning the substrate selectivity of an enzymatic reaction by directed mutagenesis can lead to higher turnover rates. This work presents a novel approach to predict the conformation of a side chain mutation along with the energetic effect on the protein structure. The HYDE scoring concept applied here describes the molecular interactions primarily by evaluating the effect of dehydration and hydrogen bonding on molecular structures in aqueous solution. Here, we evaluate its capability of side-chain conformation prediction in classic remutation experiments. Furthermore, we present a new data set for evaluating "cross-mutations," a new experiment that resembles real-world application scenarios more closely. This data set consists of protein pairs with up to five point mutations. Thus, structural changes are attributed to point mutations only. In the cross-mutation experiment, the original protein structure is mutated with the aim to predict the structure of the side chain as in the paired mutated structure. The comparison of side chain conformation prediction ("remutation") showed that the performance of HYDE
- Published
- 2017
25. Facing the Challenges of Structure-Based Target Prediction by Inverse Virtual Screening
- Author
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Sascha Urbaczek, Hans Briem, Stefan Bietz, Matthias Rarey, Angela M. Henzler, and Karen T. Schomburg
- Subjects
Protein Conformation ,Computer science ,General Chemical Engineering ,Inverse ,Library and Information Sciences ,Ligands ,computer.software_genre ,Machine learning ,Prediction methods ,Screening method ,Cutoff ,Databases, Protein ,Virtual screening ,Binding Sites ,business.industry ,Proteins ,General Chemistry ,Computer Science Applications ,Molecular Docking Simulation ,Docking (molecular) ,Drug Design ,Structure based ,Pairwise comparison ,Data mining ,Artificial intelligence ,business ,computer ,Algorithms ,Software ,Protein Binding - Abstract
Computational target prediction for bioactive compounds is a promising field in assessing off-target effects. Structure-based methods not only predict off-targets, but, simultaneously, binding modes, which are essential for understanding the mode of action and rationally designing selective compounds. Here, we highlight the current open challenges of computational target prediction methods based on protein structures and show why inverse screening rather than sequential pairwise protein-ligand docking methods are needed. A new inverse screening method based on triangle descriptors is introduced: iRAISE (inverse Rapid Index-based Screening Engine). A Scoring Cascade considering the reference ligand as well as the ligand and active site coverage is applied to overcome interprotein scoring noise of common protein-ligand scoring functions. Furthermore, a statistical evaluation of a score cutoff for each individual protein pocket is used. The ranking and binding mode prediction capabilities are evaluated on different datasets and compared to inverse docking and pharmacophore-based methods. On the Astex Diverse Set, iRAISE ranks more than 35% of the targets to the first position and predicts more than 80% of the binding modes with a root-mean-square deviation (RMSD) accuracy of2.0 Å. With a median computing time of 5 s per protein, large amounts of protein structures can be screened rapidly. On a test set with 7915 protein structures and 117 query ligands, iRAISE predicts the first true positive in a ranked list among the top eight ranks (median), i.e., among 0.28% of the targets.
- Published
- 2014
26. 11th German Conference on Chemoinformatics (GCC 2015) : Fulda, Germany. 8-10 November 2015
- Author
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Uli Fechner, Chris de Graaf, Andrew E. Torda, Stefan Güssregen, Andreas Evers, Hans Matter, Gerhard Hessler, Nicola J. Richmond, Peter Schmidtke, Marwin H. S. Segler, Mark P. Waller, Stefanie Pleik, Joan-Emma Shea, Zachary Levine, Ryan Mullen, Karina van den Broek, Matthias Epple, Hubert Kuhn, Andreas Truszkowski, Achim Zielesny, Johannes Fraaije, Ruben Serral Gracia, Stefan M. Kast, Krishna C. Bulusu, Andreas Bender, Abraham Yosipof, Oren Nahum, Hanoch Senderowitz, Timo Krotzky, Robert Schulz, Gerhard Wolber, Stefan Bietz, Matthias Rarey, Markus O. Zimmermann, Andreas Lange, Manuel Ruff, Johannes Heidrich, Ionut Onlia, Thomas E. Exner, Frank M. Boeckler, Marcel Bermudez, Dzmitry S. Firaha, Oldamur Hollóczki, Barbara Kirchner, Christofer S. Tautermann, Andrea Volkamer, Sameh Eid, Samo Turk, Friedrich Rippmann, Simone Fulle, Noureldin Saleh, Giorgio Saladino, Francesco L. Gervasio, Elke Haensele, Lee Banting, David C. Whitley, Jana Sopkova-de Oliveira Santos, Ronan Bureau, Timothy Clark, Achim Sandmann, Harald Lanig, Patrick Kibies, Jochen Heil, Franziska Hoffgaard, Roland Frach, Julian Engel, Steven Smith, Debjit Basu, Daniel Rauh, Oliver Kohlbacher, Jonathan W. Essex, Michael S. Bodnarchuk, Gregory A. Ross, Arndt R. Finkelmann, Andreas H. Göller, Gisbert Schneider, Tamara Husch, Christoph Schütter, Andrea Balducci, Martin Korth, Fidele Ntie-Kang, Stefan Günther, Wolfgang Sippl, Luc Meva’a Mbaze, Conrad V. Simoben, Lydia L. Lifongo, Philip Judson, Jiří Barilla, Miloš V. Lokajíček, Hana Pisaková, Pavel Simr, Natalia Kireeva, Alexandre Petrov, Denis Ostroumov, Vitaly P. Solovev, Vladislav S. Pervov, Nils-Ole Friedrich, Kai Sommer, Johannes Kirchmair, Eugen Proschak, Julia Weber, Daniel Moser, Lena Kalinowski, Janosch Achenbach, Mark Mackey, Tim Cheeseright, Gerrit Renner, Torsten C. Schmidt, Jürgen Schram, Marion Egelkraut-Holtus, Albert van Oeyen, Tuomo Kalliokoski, Denis Fourches, Akachukwu Ibezim, Chika J. Mbah, Umale M. Adikwu, Ngozi J. Nwodo, Alexander Steudle, Brian B. Masek, Stephan Nagy, David Baker, Fred Soltanshahi, Roman Dorfman, Karen Dubrucq, Hitesh Patel, Oliver Koch, Florian Mrugalla, Qurrat U. Ain, Julian E. Fuchs, Robert M. Owen, Kiyoyuki Omoto, Rubben Torella, David C. Pryde, Robert Glen, Petr Hošek, Vojtěch Spiwok, Lewis H. Mervin, Ian Barrett, Mike Firth, David C. Murray, Lisa McWilliams, Qing Cao, Ola Engkvist, Dawid Warszycki, Marek Śmieja, Andrzej J. Bojarski, Natalia Aniceto, Alex Freitas, Taravat Ghafourian, Guido Herrmann, Valentina Eigner-Pitto, Alexandra Naß, Rafał Kurczab, Marcel B. Günther, Susanne Hennig, Felix M. Büttner, Christoph Schall, Adrian Sievers-Engler, Francesco Ansideri, Pierre Koch, Thilo Stehle, Stefan Laufer, Frank M. Böckler, Barbara Zdrazil, Floriane Montanari, Gerhard F. Ecker, Christoph Grebner, Anders Hogner, Johan Ulander, Karl Edman, Victor Guallar, Christian Tyrchan, Wolfgang Klute, Fredrik Bergström, Christian Kramer, Quoc Dat Nguyen, Steven Strohfeldt, Saraphina Böttcher, Tim Pongratz, Dominik Horinek, Bernd Rupp, Raed Al-Yamori, Michael Lisurek, Ronald Kühne, Filipe Furtado, Ludger Wessjohann, Miriam Mathea, Knut Baumann, Siti Zuraidah Mohamad-Zobir, Xianjun Fu, Tai-Ping Fan, Maximilian A. Kuhn, Christoph A. Sotriffer, Azedine Zoufir, Xitong Li, Lewis Mervin, Ellen Berg, Mark Polokoff, Wolf D. Ihlenfeldt, Jette Pretzel, Zayan Alhalabi, Robert Fraczkiewicz, Marvin Waldman, Robert D. Clark, Neem Shaikh, Prabha Garg, Alexander Kos, Hans-Jürgen Himmler, Christophe Jardin, Heinrich Sticht, Thomas B. Steinbrecher, Markus Dahlgren, Daniel Cappel, Teng Lin, Lingle Wang, Goran Krilov, Robert Abel, Richard Friesner, Woody Sherman, Ina A. Pöhner, Joanna Panecka, Rebecca C. Wade, Karen T. Schomburg, Matthias Hilbig, Christian Jäger, Vivien Wieczorek, Lance M. Westerhoff, Oleg Y. Borbulevych, Hans-Ulrich Demuth, Mirko Buchholz, Denis Schmidt, Thomas Rickmeyer, Peter Kolb, Sumit Mittal, Elsa Sánchez-García, Mauro S. Nogueira, Tiago B. Oliveira, Fernando B. da Costa, and Thomas J. Schmidt
- Subjects
0303 health sciences ,Philosophy ,Library and Information Sciences ,16. Peace & justice ,Bioinformatics ,01 natural sciences ,Computer Graphics and Computer-Aided Design ,Meeting Abstracts ,language.human_language ,0104 chemical sciences ,Computer Science Applications ,German ,010404 medicinal & biomolecular chemistry ,03 medical and health sciences ,language ,Physical and Theoretical Chemistry ,Humanities ,030304 developmental biology - Abstract
Author(s): Fechner, Uli; de Graaf, Chris; Torda, Andrew E; Gussregen, Stefan; Evers, Andreas; Matter, Hans; Hessler, Gerhard; Richmond, Nicola J; Schmidtke, Peter; Segler, Marwin HS; Waller, Mark P; Pleik, Stefanie; Shea, Joan-Emma; Levine, Zachary; Mullen, Ryan; van den Broek, Karina; Epple, Matthias; Kuhn, Hubert; Truszkowski, Andreas; Zielesny, Achim; Fraaije, Johannes Hans; Gracia, Ruben Serral; Kast, Stefan M; Bulusu, Krishna C; Bender, Andreas; Yosipof, Abraham; Nahum, Oren; Senderowitz, Hanoch; Krotzky, Timo; Schulz, Robert; Wolber, Gerhard; Bietz, Stefan; Rarey, Matthias; Zimmermann, Markus O; Lange, Andreas; Ruff, Manuel; Heidrich, Johannes; Onlia, Ionut; Exner, Thomas E; Boeckler, Frank M; Bermudez, Marcel; Firaha, Dzmitry S; Holloczki, Oldamur; Kirchner, Barbara; Tautermann, Christofer S; Volkamer, Andrea; Eid, Sameh; Turk, Samo; Rippmann, Friedrich; Fulle, Simone; Saleh, Noureldin; Saladino, Giorgio; Gervasio, Francesco L; Haensele, Elke; Banting, Lee; Whitley, David C; Oliveira Santos, Jana Sopkova-de; Bureau, Ronan; Clark, Timothy; Sandmann, Achim; Lanig, Harald; Kibies, Patrick; Heil, Jochen; Hoffgaard, Franziska; Frach, Roland; Engel, Julian; Smith, Steven; Basu, Debjit; Rauh, Daniel; Kohlbacher, Oliver; Boeckler, Frank M; Essex, Jonathan W; Bodnarchuk, Michael S; Ross, Gregory A; Finkelmann, Arndt R; Goller, Andreas H; Schneider, Gisbert; Husch, Tamara; Schutter, Christoph; Balducci, Andrea; Korth, Martin; Ntie-Kang, Fidele; Gunther, Stefan; Sippl, Wolfgang; Mbaze, Luc Meva'a
- Published
- 2016
27. SIENA: Efficient Compilation of Selective Protein Binding Site Ensembles
- Author
-
Matthias Rarey and Stefan Bietz
- Subjects
0301 basic medicine ,Models, Molecular ,Computer science ,Protein Conformation ,General Chemical Engineering ,Plasma protein binding ,Computational biology ,Library and Information Sciences ,Substrate Specificity ,Alternative protein ,03 medical and health sciences ,Molecular recognition ,Protein structure ,Preprocessor ,Data Mining ,Binding site ,Databases, Protein ,Binding Sites ,Computational Biology ,Proteins ,General Chemistry ,Computer Science Applications ,030104 developmental biology ,Data Annotation ,Algorithm ,Function (biology) ,Algorithms ,Software ,Protein Binding - Abstract
Structural flexibility of proteins has an important influence on molecular recognition and enzymatic function. In modeling, structure ensembles are therefore often applied as a valuable source of alternative protein conformations. However, their usage is often complicated by structural artifacts and inconsistent data annotation. Here, we present SIENA, a new computational approach for the automated assembly and preprocessing of protein binding site ensembles. Starting with an arbitrarily defined binding site in a single protein structure, SIENA searches for alternative conformations of the same or sequentially closely related binding sites. The method is based on an indexed database for identifying perfect k-mer matches and a recently published algorithm for the alignment of protein binding site conformations. Furthermore, SIENA provides a new algorithm for the interaction-based selection of binding site conformations which aims at covering all known ligand-binding geometries. Various experiments highlight that SIENA is able to generate comprehensive and well selected binding site ensembles improving the compatibility to both known and unconsidered ligand molecules. Starting with the whole PDB as data source, the computation time of the whole ensemble generation takes only a few seconds. SIENA is available via a Web service at www.zbh.uni-hamburg.de/siena .
- Published
- 2016
28. ASCONA: Rapid Detection and Alignment of Protein Binding Site Conformations
- Author
-
Matthias Rarey and Stefan Bietz
- Subjects
Protein Conformation ,General Chemical Engineering ,Structural alignment ,Computational biology ,Plasma protein binding ,Library and Information Sciences ,Biology ,Machine learning ,computer.software_genre ,Ligands ,Rapid detection ,Search algorithm ,Animals ,Humans ,Amino Acid Sequence ,Binding site ,Databases, Protein ,Conformational ensembles ,Flexibility (engineering) ,Binding Sites ,business.industry ,Proteins ,General Chemistry ,Computer Science Applications ,Molecular Docking Simulation ,Artificial intelligence ,business ,computer ,Algorithms ,Protein ligand ,Protein Binding - Abstract
The usage of conformational ensembles constitutes a widespread technique for the consideration of protein flexibility in computational biology. When experimental structures are applied for this purpose, alignment techniques are usually required in dealing with structural deviations and annotation inconsistencies. Moreover, many application scenarios focus on protein ligand binding sites. Here, we introduce our new alignment algorithm ASCONA that has been specially geared to the problem of aligning multiple conformations of sequentially similar binding sites. Intense efforts have been directed to an accurate detection of highly flexible backbone deviations, multiple binding site matches within a single structure, and a reliable, but at the same time highly efficient, search algorithm. In contrast, most available alignment methods rather target other issues, e.g., the global alignment of distantly related proteins that share structurally conserved regions. For conformational ensembles, this might not only result in an overhead of computation time but could also affect the achieved accuracy, especially for more complicated cases as highly flexible proteins. ASCONA was evaluated on a test set containing 1107 structures of 65 diverse proteins. In all cases, ASCONA was able to correctly align the binding site at an average alignment computation time of 4 ms per target. Furthermore, no false positive matches were observed when searching the same query sites in the structures of other proteins. ASCONA proved to cope with highly deviating backbone structures and to tolerate structural gaps and moderate mutation rates. ASCONA is available free of charge for academic use at http://www.zbh.uni-hamburg.de/ascona .
- Published
- 2015
29. Protoss: a holistic approach to predict tautomers and protonation states in protein-ligand complexes
- Author
-
Sascha Urbaczek, Benjamin L. Schulz, Matthias Rarey, and Stefan Bietz
- Subjects
Hydrogen ,Ligand ,Hydrogen bond ,Chemistry ,Binding energy ,Tautomers ,Degrees of freedom (statistics) ,chemistry.chemical_element ,Nanotechnology ,Protonation ,Hydrogen placement ,Library and Information Sciences ,Protein-ligand complex ,Computer Graphics and Computer-Aided Design ,Tautomer ,Computer Science Applications ,Chemical physics ,Protonation states ,Physical and Theoretical Chemistry ,Research Article ,Protein ligand - Abstract
Abstract The calculation of hydrogen positions is a common preprocessing step when working with crystal structures of protein-ligand complexes. An explicit description of hydrogen atoms is generally needed in order to analyze the binding mode of particular ligands or to calculate the associated binding energies. Due to the large number of degrees of freedom resulting from different chemical moieties and the high degree of mutual dependence this problem is anything but trivial. In addition to an efficient algorithm to take care of the complexity resulting from complicated hydrogen bonding networks, a robust chemical model is needed to describe effects such as tautomerism and ionization consistently. We present a novel method for the placement of hydrogen coordinates in protein-ligand complexes which takes tautomers and protonation states of both protein and ligand into account. Our method generates the most probable hydrogen positions on the basis of an optimal hydrogen bonding network using an empirical scoring function. The high quality of our results could be verified by comparison to the manually adjusted Astex diverse set and a remarkably low rate of undesirable hydrogen contacts compared to other tools.
- Published
- 2014
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