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Sorzano COS, Semchonok D, Lin SC, Lo YC, Vilas JL, Jiménez-Moreno A, Gragera M, Vacca S, Maluenda D, Martínez M, Ramírez-Aportela E, Melero R, Cuervo A, Conesa JJ, Conesa P, Losana P, Caño LD, de la Morena JJ, Fonseca YC, Sánchez-García R, Strelak D, Fernández-Giménez E, de Isidro F, Herreros D, Kastritis PL, Marabini R, Bruce BD, Carazo JM. Algorithmic robustness to preferred orientations in single particle analysis by CryoEM. J Struct Biol 2021; 213:107695. [PMID: 33421545 DOI: 10.1016/j.jsb.2020.107695] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 12/18/2020] [Accepted: 12/24/2020] [Indexed: 01/30/2023]
Abstract
The presence of preferred orientations in single particle analysis (SPA) by cryo-Electron Microscopy (cryoEM) is currently one of the hurdles preventing many structural analyses from yielding high-resolution structures. Although the existence of preferred orientations is mostly related to the grid preparation, in this technical note, we show that some image processing algorithms used for angular assignment and three-dimensional (3D) reconstruction are more robust than others to these detrimental conditions. We exemplify this argument with three different data sets in which the presence of preferred orientations hindered achieving a 3D reconstruction without artifacts or, even worse, a 3D reconstruction could never be achieved.
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Affiliation(s)
- C O S Sorzano
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain.
| | - D Semchonok
- ZIK HALOMEM & Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Biozentrum, Halle (Saale), Germany
| | - S-C Lin
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Y-C Lo
- Dept. Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - J L Vilas
- Dept. of Biomedical Engineering, Yale University, New Haven, United States
| | - A Jiménez-Moreno
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - M Gragera
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - S Vacca
- Dept. of Biochemistry, Univ. Zurich, Winterthurerstr. 190, CH-8057 Zurich, Switzerland
| | - D Maluenda
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - M Martínez
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - E Ramírez-Aportela
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - R Melero
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - A Cuervo
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - J J Conesa
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - P Conesa
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - P Losana
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - L Del Caño
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - J Jiménez de la Morena
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - Y C Fonseca
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - R Sánchez-García
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - D Strelak
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - E Fernández-Giménez
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - F de Isidro
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - D Herreros
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - P L Kastritis
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - R Marabini
- Escuela Politecnica Superior, Universidad Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain
| | - B D Bruce
- Dept. Biochemistry & Cellular and Molecular Biology, Univ. Tennessee Knoxville, Knoxville, TN 37996, United States
| | - J M Carazo
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
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2
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Vangone A, Rodrigues JPGLM, Xue LC, van Zundert GCP, Geng C, Kurkcuoglu Z, Nellen M, Narasimhan S, Karaca E, van Dijk M, Melquiond ASJ, Visscher KM, Trellet M, Kastritis PL, Bonvin AMJJ. Sense and Simplicity in HADDOCK Scoring: Lessons from CASP-CAPRI (page 418). Proteins 2017; 85:1589-1590. [PMID: 28730688 DOI: 10.1002/prot.25339] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- A Vangone
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands
| | - J P G L M Rodrigues
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands
| | - L C Xue
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands
| | - G C P van Zundert
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands
| | - C Geng
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands
| | - Z Kurkcuoglu
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands
| | - M Nellen
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands
| | - S Narasimhan
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands
| | - E Karaca
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands
| | - M van Dijk
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands
| | - A S J Melquiond
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands
| | - K M Visscher
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands
| | - M Trellet
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands
| | - P L Kastritis
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands
| | - A M J J Bonvin
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands
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3
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Vangone A, Rodrigues JPGLM, Xue LC, van Zundert GCP, Geng C, Kurkcuoglu Z, Nellen M, Narasimhan S, Karaca E, van Dijk M, Melquiond ASJ, Visscher KM, Trellet M, Kastritis PL, Bonvin AMJJ. Sense and simplicity in HADDOCK scoring: Lessons from CASP-CAPRI round 1. Proteins 2016; 85:417-423. [PMID: 27802573 PMCID: PMC5324763 DOI: 10.1002/prot.25198] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/14/2016] [Accepted: 10/25/2016] [Indexed: 12/28/2022]
Abstract
Our information-driven docking approach HADDOCK is a consistent top predictor and scorer since the start of its participation in the CAPRI community-wide experiment. This sustained performance is due, in part, to its ability to integrate experimental data and/or bioinformatics information into the modelling process, and also to the overall robustness of the scoring function used to assess and rank the predictions. In the CASP-CAPRI Round 1 scoring experiment we successfully selected acceptable/medium quality models for 18/14 of the 25 targets - a top-ranking performance among all scorers. Considering that for only 20 targets acceptable models were generated by the community, our effective success rate reaches as high as 90% (18/20). This was achieved using the standard HADDOCK scoring function, which, thirteen years after its original publication, still consists of a simple linear combination of intermolecular van der Waals and Coulomb electrostatics energies and an empirically derived desolvation energy term. Despite its simplicity, this scoring function makes sense from a physico-chemical perspective, encoding key aspects of biomolecular recognition. In addition to its success in the scoring experiment, the HADDOCK server takes the first place in the server prediction category, with 16 successful predictions. Much like our scoring protocol, because of the limited time per target, the predictions relied mainly on either an ab initio center-of-mass and symmetry restrained protocol, or on a template-based approach whenever applicable. These results underline the success of our simple but sensible prediction and scoring scheme. Proteins 2017; 85:417-423. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- A Vangone
- Department of Chemistry, Computational Structural Biology Group, Faculty of Science, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
| | - J P G L M Rodrigues
- Department of Chemistry, Computational Structural Biology Group, Faculty of Science, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
| | - L C Xue
- Department of Chemistry, Computational Structural Biology Group, Faculty of Science, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
| | - G C P van Zundert
- Department of Chemistry, Computational Structural Biology Group, Faculty of Science, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
| | - C Geng
- Department of Chemistry, Computational Structural Biology Group, Faculty of Science, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
| | - Z Kurkcuoglu
- Department of Chemistry, Computational Structural Biology Group, Faculty of Science, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
| | - M Nellen
- Department of Chemistry, Computational Structural Biology Group, Faculty of Science, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
| | - S Narasimhan
- Department of Chemistry, Computational Structural Biology Group, Faculty of Science, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
| | - E Karaca
- Department of Chemistry, Computational Structural Biology Group, Faculty of Science, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
| | - M van Dijk
- Department of Chemistry, Computational Structural Biology Group, Faculty of Science, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
| | - A S J Melquiond
- Department of Chemistry, Computational Structural Biology Group, Faculty of Science, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
| | - K M Visscher
- Department of Chemistry, Computational Structural Biology Group, Faculty of Science, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
| | - M Trellet
- Department of Chemistry, Computational Structural Biology Group, Faculty of Science, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
| | - P L Kastritis
- Department of Chemistry, Computational Structural Biology Group, Faculty of Science, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
| | - A M J J Bonvin
- Department of Chemistry, Computational Structural Biology Group, Faculty of Science, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
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4
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van Zundert GCP, Rodrigues JPGLM, Trellet M, Schmitz C, Kastritis PL, Karaca E, Melquiond ASJ, van Dijk M, de Vries SJ, Bonvin AMJJ. The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes. J Mol Biol 2016; 428:720-725. [PMID: 26410586 DOI: 10.1016/j.jmb.2015.09.014)] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 09/16/2015] [Accepted: 09/17/2015] [Indexed: 05/23/2023]
Abstract
The prediction of the quaternary structure of biomolecular macromolecules is of paramount importance for fundamental understanding of cellular processes and drug design. In the era of integrative structural biology, one way of increasing the accuracy of modeling methods used to predict the structure of biomolecular complexes is to include as much experimental or predictive information as possible in the process. This has been at the core of our information-driven docking approach HADDOCK. We present here the updated version 2.2 of the HADDOCK portal, which offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in a user-friendly interface. With well over 6000 registered users and 108,000 jobs served, an increasing fraction of which on grid resources, we hope that this timely upgrade will help the community to solve important biological questions and further advance the field. The HADDOCK2.2 Web server is freely accessible to non-profit users at http://haddock.science.uu.nl/services/HADDOCK2.2.
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Affiliation(s)
- G C P van Zundert
- Bijvoet Center for Biomolecular Research, Faculty of Science Department of Chemistry, Utrecht University, Domplein 29, 3512 JE Utrecht, the Netherlands
| | - J P G L M Rodrigues
- Bijvoet Center for Biomolecular Research, Faculty of Science Department of Chemistry, Utrecht University, Domplein 29, 3512 JE Utrecht, the Netherlands
| | - M Trellet
- Centre National de la Recherche Scientifique Laboratoire d'Informatique pour la Mécanique et les Sciences de l'Ingénieur, rue John Von Neumann, 91403 Orsay, France
| | - C Schmitz
- Instaclustr Level 5, 1 Moore Street, Canberra ACT 2600, Australia
| | - P L Kastritis
- European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - E Karaca
- European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - A S J Melquiond
- Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - M van Dijk
- Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, the Netherlands
| | - S J de Vries
- Physik-Department, Technische Universität München, James-Franck-Strasse 1, 85748 Garching, Germany
| | - A M J J Bonvin
- Bijvoet Center for Biomolecular Research, Faculty of Science Department of Chemistry, Utrecht University, Domplein 29, 3512 JE Utrecht, the Netherlands
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5
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van Zundert GCP, Rodrigues JPGLM, Trellet M, Schmitz C, Kastritis PL, Karaca E, Melquiond ASJ, van Dijk M, de Vries SJ, Bonvin AMJJ. The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes. J Mol Biol 2015; 428:720-725. [PMID: 26410586 DOI: 10.1016/j.jmb.2015.09.014] [Citation(s) in RCA: 1659] [Impact Index Per Article: 184.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 09/16/2015] [Accepted: 09/17/2015] [Indexed: 11/25/2022]
Abstract
The prediction of the quaternary structure of biomolecular macromolecules is of paramount importance for fundamental understanding of cellular processes and drug design. In the era of integrative structural biology, one way of increasing the accuracy of modeling methods used to predict the structure of biomolecular complexes is to include as much experimental or predictive information as possible in the process. This has been at the core of our information-driven docking approach HADDOCK. We present here the updated version 2.2 of the HADDOCK portal, which offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in a user-friendly interface. With well over 6000 registered users and 108,000 jobs served, an increasing fraction of which on grid resources, we hope that this timely upgrade will help the community to solve important biological questions and further advance the field. The HADDOCK2.2 Web server is freely accessible to non-profit users at http://haddock.science.uu.nl/services/HADDOCK2.2.
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Affiliation(s)
- G C P van Zundert
- Bijvoet Center for Biomolecular Research, Faculty of Science Department of Chemistry, Utrecht University, Domplein 29, 3512 JE Utrecht, the Netherlands
| | - J P G L M Rodrigues
- Bijvoet Center for Biomolecular Research, Faculty of Science Department of Chemistry, Utrecht University, Domplein 29, 3512 JE Utrecht, the Netherlands
| | - M Trellet
- Centre National de la Recherche Scientifique Laboratoire d'Informatique pour la Mécanique et les Sciences de l'Ingénieur, rue John Von Neumann, 91403 Orsay, France
| | - C Schmitz
- Instaclustr Level 5, 1 Moore Street, Canberra ACT 2600, Australia
| | - P L Kastritis
- European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - E Karaca
- European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - A S J Melquiond
- Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - M van Dijk
- Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, the Netherlands
| | - S J de Vries
- Physik-Department, Technische Universität München, James-Franck-Strasse 1, 85748 Garching, Germany
| | - A M J J Bonvin
- Bijvoet Center for Biomolecular Research, Faculty of Science Department of Chemistry, Utrecht University, Domplein 29, 3512 JE Utrecht, the Netherlands
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6
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Rodrigues JPGLM, Melquiond ASJ, Karaca E, Trellet M, van Dijk M, van Zundert GCP, Schmitz C, de Vries SJ, Bordogna A, Bonati L, Kastritis PL, Bonvin AMJJ. Defining the limits of homology modeling in information-driven protein docking. Proteins 2013; 81:2119-28. [PMID: 23913867 DOI: 10.1002/prot.24382] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 07/16/2013] [Accepted: 07/25/2013] [Indexed: 12/28/2022]
Abstract
Information-driven docking is currently one of the most successful approaches to obtain structural models of protein interactions as demonstrated in the latest round of CAPRI. While various experimental and computational techniques can be used to retrieve information about the binding mode, the availability of three-dimensional structures of the interacting partners remains a limiting factor. Fortunately, the wealth of structural information gathered by large-scale initiatives allows for homology-based modeling of a significant fraction of the protein universe. Defining the limits of information-driven docking based on such homology models is therefore highly relevant. Here we show, using previous CAPRI targets, that out of a variety of measures, the global sequence identity between template and target is a simple but reliable predictor of the achievable quality of the docking models. This indicates that a well-defined overall fold is critical for the interaction. Furthermore, the quality of the data at our disposal to characterize the interaction plays a determinant role in the success of the docking. Given reliable interface information we can obtain acceptable predictions even at low global sequence identity. These results, which define the boundaries between trustworthy and unreliable predictions, should guide both experts and nonexperts in defining the limits of what is achievable by docking. This is highly relevant considering that the fraction of the interactome amenable for docking is only bound to grow as the number of experimentally solved structures increases.
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Affiliation(s)
- J P G L M Rodrigues
- Faculty of Science/Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, 3584CH, The Netherlands
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