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Honorato RV, Trellet ME, Jiménez-García B, Schaarschmidt JJ, Giulini M, Reys V, Koukos PI, Rodrigues JPGLM, Karaca E, van Zundert GCP, Roel-Touris J, van Noort CW, Jandová Z, Melquiond ASJ, Bonvin AMJJ. The HADDOCK2.4 web server for integrative modeling of biomolecular complexes. Nat Protoc 2024; 19:3219-3241. [PMID: 38886530 DOI: 10.1038/s41596-024-01011-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 04/11/2024] [Indexed: 06/20/2024]
Abstract
Interactions between macromolecules, such as proteins and nucleic acids, are essential for cellular functions. Experimental methods can fail to provide all the information required to fully model biomolecular complexes at atomic resolution, particularly for large and heterogeneous assemblies. Integrative computational approaches have, therefore, gained popularity, complementing traditional experimental methods in structural biology. Here, we introduce HADDOCK2.4, an integrative modeling platform, and its updated web interface ( https://wenmr.science.uu.nl/haddock2.4 ). The platform seamlessly integrates diverse experimental and theoretical data to generate high-quality models of macromolecular complexes. The user-friendly web server offers automated parameter settings, access to distributed computing resources, and pre- and post-processing steps that enhance the user experience. To present the web server's various interfaces and features, we demonstrate two different applications: (i) we predict the structure of an antibody-antigen complex by using NMR data for the antigen and knowledge of the hypervariable loops for the antibody, and (ii) we perform coarse-grained modeling of PRC1 with a nucleosome particle guided by mutagenesis and functional data. The described protocols require some basic familiarity with molecular modeling and the Linux command shell. This new version of our widely used HADDOCK web server allows structural biologists and non-experts to explore intricate macromolecular assemblies encompassing various molecule types.
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Affiliation(s)
- Rodrigo V Honorato
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Mikael E Trellet
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- Fluigent, Le Kremlin-Bicêtre, France
| | - Brian Jiménez-García
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- Zymvol Biomodeling SL, Barcelona, Spain
| | - Jörg J Schaarschmidt
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- Karlsruhe Institute of Technology (KIT), Institute of Nanotechnology, Eggenstein-Leopoldshafen, Germany
| | - Marco Giulini
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Victor Reys
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Panagiotis I Koukos
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - João P G L M Rodrigues
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- Schrödinger Inc., New York, NY, USA
| | - Ezgi Karaca
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- Izmir Biomedicine and Genome Center, Izimir, Turkey
| | - Gydo C P van Zundert
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- Schrödinger Inc., New York, NY, USA
| | - Jorge Roel-Touris
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- Protein Design and Modeling Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, Spain
| | - Charlotte W van Noort
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Zuzana Jandová
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- Boehringer Ingelheim International GmbH, Vienna, Austria
| | - Adrien S J Melquiond
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- Utrecht Medical Center, Utrecht, the Netherlands
| | - Alexandre M J J Bonvin
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.
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2
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Mansinhbhai CH, Sakure A, Liu Z, Maurya R, Das S, Basaiawmoit B, Bishnoi M, Kondepudi KK, Padhi S, Rai AK, Mishra BK, Hati S. Anti-Inflammatory, ACE Inhibitory, Antioxidative Activities and Release of Novel Antihypertensive and Antioxidative Peptides from Whey Protein Hydrolysate with Molecular Interactions. JOURNAL OF THE AMERICAN NUTRITION ASSOCIATION 2023; 42:371-385. [PMID: 35584265 DOI: 10.1080/07315724.2022.2052201] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
OBJECTIVE The aim of the study was to evaluate the whey protein hydrolysate with bio-functional attributes viz. antioxidative, anti-inflammatory and ACE inhibition efficacy and release of bioactive peptides with antioxidative and ACE-inhibitory activity by employing Pepsin. METHOD The antioxidant, Anti-inflammatory, ACE inhibitory and proteolytic activities of the whey protein hydrolysates were studied followed by SDS-PAGE analysis and IEF. Anti-inflammatory activity of whey protein hydrolysate was also studied on RAW 264.7 cell line. The separation of the bioactive peptides from whey protein hydrolysate was achieved by RP-HPLC. The purified bioactive peptides were identified and characterized using RPLC/MS. RESULTS WPC (Whey protein concentrate) hydrolysate with pepsin showed proteolytic activity ranging between 14.46 and 18.87 mg/ml. Using the ABTS assay, the highest antioxidative activity was observed in 10 kDa retentate (84.50%) and 3 kDa retentate (85.96%), followed by the highest proteolytic activity (13.83 mg/ml) and ACE inhibitory activity (58.37%) in a 5% WPC solution at 65 °C after 8 h of pepsin hydrolysis. When the protein hydrolysate concentration was low, the production of proinflammatory cytokines by lipopolysaccharide-treated murine macrophages (RAW 264.7) was reduced. SDS-PAGE results exhibited very little protein bands when comparing with WPC hydrolysates to insoluble WPC. There were no protein spots on 2 D gel electrophoresis and "in-solution trypsin digestion" technique have been utilized to digest protein samples directly from WPC hydrolysates. Novel antioxidative peptides and ACE inhibitory peptides were also observed by comparing two databases, i.e., BIOPEP and AHTPDB respectively. The peptide sequences used in this study were found to have excellent potential to be used as inhibitors of hACE as all of them were able to show substantial interactions against the enzyme's active site. CONCLUSIONS The antihypertensive and antioxidative peptides from whey protein hydrolysates may be beneficial for the future development of physiologically active functional foods. Further, in vivo investigations are required to establish the health claim for each individual bioactive peptide from whey protein hydrolysate. Supplemental data for this article is available online at.
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Affiliation(s)
| | - Amar Sakure
- Department of Agriculture Biotechnology, Anand Agricultural University, Anand, Gujarat, India
| | - Zhenbin Liu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Ruchika Maurya
- Regional Center for Biotechnology, Faridabad, Haryana, India
- Healthy Gut Research Group, Food & Nutritional Biotechnology Division, National Agri-Food Biotechnology Institute, Knowledge City, Punjab, India
| | - Sujit Das
- Department of Rural Development and Agricultural Production, North-Eastern Hill University, Tura, Meghalaya, India
| | - Bethsheba Basaiawmoit
- Department of Rural Development and Agricultural Production, North-Eastern Hill University, Tura, Meghalaya, India
| | - Mahendra Bishnoi
- Healthy Gut Research Group, Food & Nutritional Biotechnology Division, National Agri-Food Biotechnology Institute, Knowledge City, Punjab, India
| | - Kanthi Kiran Kondepudi
- Healthy Gut Research Group, Food & Nutritional Biotechnology Division, National Agri-Food Biotechnology Institute, Knowledge City, Punjab, India
| | - Srichandan Padhi
- Institute of Bioresources and Sustainable Development, Regional Centre, Tadong, Sikkim, India
| | - Amit Kumar Rai
- Institute of Bioresources and Sustainable Development, Regional Centre, Tadong, Sikkim, India
| | - Birendra K Mishra
- Department of Rural Development and Agricultural Production, North-Eastern Hill University, Tura, Meghalaya, India
| | - Subrota Hati
- Department of Dairy Microbiology, SMC College of Dairy Science, Kamdhenu University, Anand, Gujarat, India
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3
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Koukos P, Bonvin A. Integrative Modelling of Biomolecular Complexes. J Mol Biol 2020; 432:2861-2881. [DOI: 10.1016/j.jmb.2019.11.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 11/12/2019] [Accepted: 11/13/2019] [Indexed: 12/31/2022]
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4
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Morris C, Andreetto P, Banci L, Bonvin AMJJ, Chojnowski G, Cano LD, Carazo JM, Conesa P, Daenke S, Damaskos G, Giachetti A, Haley NEC, Hekkelman ML, Heuser P, Joosten RP, Kouřil D, Křenek A, Kulhánek T, Lamzin VS, Nadzirin N, Perrakis A, Rosato A, Sanderson F, Segura J, Schaarschmidt J, Sobolev E, Traldi S, Trellet ME, Velankar S, Verlato M, Winn M. West-Life: A Virtual Research Environment for structural biology. JOURNAL OF STRUCTURAL BIOLOGY-X 2019; 1:100006. [PMID: 32647812 PMCID: PMC7337051 DOI: 10.1016/j.yjsbx.2019.100006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Data processing and data management services for structural biology. Enhancements to existing web services for structure solution and analysis. New pipelines to link these services into more complex higher-level workflows. New data management facilities. Making the benefits of European e-Infrastructures more accessible to structural biologists.
The West-Life project (https://about.west-life.eu/) is a Horizon 2020 project funded by the European Commission to provide data processing and data management services for the international community of structural biologists, and in particular to support integrative experimental approaches within the field of structural biology. It has developed enhancements to existing web services for structure solution and analysis, created new pipelines to link these services into more complex higher-level workflows, and added new data management facilities. Through this work it has striven to make the benefits of European e-Infrastructures more accessible to life-science researchers in general and structural biologists in particular.
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Affiliation(s)
| | | | - Lucia Banci
- Magnetic Resonance Center, University of Florence, Italy
| | | | - Grzegorz Chojnowski
- European Molecular Biology Laboratory, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | | | | | | | | | - George Damaskos
- Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | - Maarten L Hekkelman
- Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Philipp Heuser
- European Molecular Biology Laboratory, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Robbie P Joosten
- Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | | | - Victor S Lamzin
- European Molecular Biology Laboratory, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Nurul Nadzirin
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Anastassis Perrakis
- Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Antonio Rosato
- Magnetic Resonance Center, University of Florence, Italy
| | | | | | | | - Egor Sobolev
- European Molecular Biology Laboratory, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | | | | | - Sameer Velankar
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
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van Zundert GCP, Hudson BM, de Oliveira SHP, Keedy DA, Fonseca R, Heliou A, Suresh P, Borrelli K, Day T, Fraser JS, van den Bedem H. qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps. J Med Chem 2018; 61:11183-11198. [PMID: 30457858 DOI: 10.1021/acs.jmedchem.8b01292] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Proteins and ligands sample a conformational ensemble that governs molecular recognition, activity, and dissociation. In structure-based drug design, access to this conformational ensemble is critical to understand the balance between entropy and enthalpy in lead optimization. However, ligand conformational heterogeneity is currently severely underreported in crystal structures in the Protein Data Bank, owing in part to a lack of automated and unbiased procedures to model an ensemble of protein-ligand states into X-ray data. Here, we designed a computational method, qFit-ligand, to automatically resolve conformationally averaged ligand heterogeneity in crystal structures, and applied it to a large set of protein receptor-ligand complexes. In an analysis of the cancer related BRD4 domain, we found that up to 29% of protein crystal structures bound with drug-like molecules present evidence of unmodeled, averaged, relatively isoenergetic conformations in ligand-receptor interactions. In many retrospective cases, these alternate conformations were adventitiously exploited to guide compound design, resulting in improved potency or selectivity. Combining qFit-ligand with high-throughput screening or multitemperature crystallography could therefore augment the structure-based drug design toolbox.
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Affiliation(s)
| | - Brandi M Hudson
- Department of Bioengineering and Therapeutic Sciences , UCSF , San Francisco , California 94158 , United States
| | - Saulo H P de Oliveira
- SLAC National Accelerator Laboratory , Stanford University , Menlo Park , California 94025 United States
| | - Daniel A Keedy
- Department of Bioengineering and Therapeutic Sciences , UCSF , San Francisco , California 94158 , United States
| | - Rasmus Fonseca
- Department of Molecular and Cellular Physiology , Stanford University , Stanford , California 94305 , United States
| | - Amelie Heliou
- LIX, Ecole Polytechnique, CNRS, Inria , Université Paris-Saclay , 91128 Palaiseau , France
| | - Pooja Suresh
- Department of Bioengineering and Therapeutic Sciences , UCSF , San Francisco , California 94158 , United States
| | | | - Tyler Day
- Schrödinger , New York , New York 10036 , United States
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences , UCSF , San Francisco , California 94158 , United States
| | - Henry van den Bedem
- Department of Bioengineering and Therapeutic Sciences , UCSF , San Francisco , California 94158 , United States.,SLAC National Accelerator Laboratory , Stanford University , Menlo Park , California 94025 United States
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6
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Wang Y, Shekhar M, Thifault D, Williams CJ, McGreevy R, Richardson J, Singharoy A, Tajkhorshid E. Constructing atomic structural models into cryo-EM densities using molecular dynamics - Pros and cons. J Struct Biol 2018; 204:319-328. [PMID: 30092279 PMCID: PMC6394829 DOI: 10.1016/j.jsb.2018.08.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 07/31/2018] [Accepted: 08/05/2018] [Indexed: 01/11/2023]
Abstract
Accurate structure determination from electron density maps at 3-5 Å resolution necessitates a balance between extensive global and local sampling of atomistic models, yet with the stereochemical correctness of backbone and sidechain geometries. Molecular Dynamics Flexible Fitting (MDFF), particularly through a resolution-exchange scheme, ReMDFF, provides a robust way of achieving this balance for hybrid structure determination. Employing two high-resolution density maps, namely that of β-galactosidase at 3.2 Å and TRPV1 at 3.4 Å, we showcase the quality of ReMDFF-generated models, comparing them against ones submitted by independent research groups for the 2015-2016 Cryo-EM Model Challenge. This comparison offers a clear evaluation of ReMDFF's strengths and shortcomings, and those of data-guided real-space refinements in general. ReMDFF results scored highly on the various metric for judging the quality-of-fit and quality-of-model. However, some systematic discrepancies are also noted employing a Molprobity analysis, that are reproducible across multiple competition entries. A space of key refinement parameters is explored within ReMDFF to observe their impact within the final model. Choice of force field parameters and initial model seem to have the most significant impact on ReMDFF model-quality. To this end, very recently developed CHARMM36m force field parameters provide now more refined ReMDFF models than the ones originally submitted to the Cryo-EM challenge. Finally, a set of good-practices is prescribed for the community to benefit from the MDFF developments.
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Affiliation(s)
- Yuhang Wang
- Center for Biophysics and Quantitative Biology, College of Medicine, Department of Biochemistry, Beckman Institute for Advanced Science and Technology, and University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Mrinal Shekhar
- Center for Biophysics and Quantitative Biology, College of Medicine, Department of Biochemistry, Beckman Institute for Advanced Science and Technology, and University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Darren Thifault
- School of Molecular Sciences, Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, United States
| | | | - Ryan McGreevy
- Center for Biophysics and Quantitative Biology, College of Medicine, Department of Biochemistry, Beckman Institute for Advanced Science and Technology, and University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Jane Richardson
- Department of Biochemistry, Duke University, Durham, NC 27710, United States
| | - Abhishek Singharoy
- School of Molecular Sciences, Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, United States.
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
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7
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Kim DN, Sanbonmatsu KY. Tools for the cryo-EM gold rush: going from the cryo-EM map to the atomistic model. Biosci Rep 2017; 37:BSR20170072. [PMID: 28963369 PMCID: PMC5715128 DOI: 10.1042/bsr20170072] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 09/26/2017] [Accepted: 09/27/2017] [Indexed: 12/16/2022] Open
Abstract
As cryo-electron microscopy (cryo-EM) enters mainstream structural biology, the demand for fitting methods is high. Here, we review existing flexible fitting methods for cryo-EM. We discuss their importance, potential concerns and assessment strategies. We aim to give readers concrete descriptions of cryo-EM flexible fitting methods with corresponding examples.
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Affiliation(s)
- Doo Nam Kim
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, U.S.A
| | - Karissa Y Sanbonmatsu
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, U.S.A.
- New Mexico Consortium, Los Alamos, U.S.A
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8
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Hoffmann A, Perrier V, Grudinin S. A novel fast Fourier transform accelerated off-grid exhaustive search method for cryo-electron microscopy fitting. J Appl Crystallogr 2017. [DOI: 10.1107/s1600576717008172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
This paper presents a novel fast Fourier transform (FFT)-based exhaustive search method extended to off-grid translational and rotational degrees of freedom. The method combines the advantages of the FFT-based exhaustive search, which samples all the conformations of a system under study on a grid, with a local optimization technique that guarantees to find the nearest optimal off-grid conformation. The method is demonstrated on a fitting problem and can be readily applied to a docking problem. The algorithm first samples a scoring function on a six-dimensional grid of sizeN6using the FFT. This operation has an asymptotic complexity ofO(N6logN). Then, the method performs the off-grid search using a local quadratic approximation of the cost function and the trust-region optimization algorithm. The computation of the quadratic approximation is also accelerated by FFT at the same additional asymptotic cost ofO(N6logN). The method is demonstrated by fitting atomic protein models into several simulated and experimental maps from cryo-electron microscopy. The method is available at https://team.inria.fr/nano-d/software/offgridfit.
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9
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van Zundert GCP, Trellet M, Schaarschmidt J, Kurkcuoglu Z, David M, Verlato M, Rosato A, Bonvin AMJJ. The DisVis and PowerFit Web Servers: Explorative and Integrative Modeling of Biomolecular Complexes. J Mol Biol 2016; 429:399-407. [PMID: 27939290 DOI: 10.1016/j.jmb.2016.11.032] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 11/29/2016] [Accepted: 11/30/2016] [Indexed: 12/13/2022]
Abstract
Structure determination of complex molecular machines requires a combination of an increasing number of experimental methods with highly specialized software geared toward each data source to properly handle the gathered data. Recently, we introduced the two software packages PowerFit and DisVis. These combine high-resolution structures of atomic subunits with density maps from cryo-electron microscopy or distance restraints, typically acquired by chemical cross-linking coupled with mass spectrometry, respectively. Here, we report on recent advances in both GPGPU-accelerated software packages: PowerFit is a tool for rigid body fitting of atomic structures in cryo-electron density maps and has been updated to also output reliability indicators for the success of fitting, through the use of the Fisher z-transformation and associated confidence intervals; DisVis aims at quantifying the information content of distance restraints and identifying false-positive restraints. We extended its analysis capabilities to include an analysis of putative interface residues and to output an average shape representing the putative location of the ligand. To facilitate their use by a broad community, they have been implemented as web portals harvesting both local CPU resources and GPGPU-accelerated EGI grid resources. They offer user-friendly interfaces, while minimizing computational requirements, and provide a first interactive view of the results. The portals can be accessed freely after registration via http://milou.science.uu.nl/services/DISVIS and http://milou.science.uu.nl/services/POWERFIT.
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Affiliation(s)
- G C P van Zundert
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - M Trellet
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - J Schaarschmidt
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - Z Kurkcuoglu
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - M David
- LIP - Laboratório de Instrumentação e Física Experimental de Particulãs, Avenida Elias Garcia 14, 1000 Lisbon, Portugal
| | - M Verlato
- Istituto Nazionale di Fisica Nucleare - Sezione di Padova, Via Marzolo 8, 35131 Padova, Italy
| | - A Rosato
- Magnetic Resonance Center and Department of Chemistry "Ugo Schiff", University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - A M J J Bonvin
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands.
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