The HDOCK server for integrated protein–protein docking

The HDOCK server ( http://hdock.phys.hust.edu.cn/ ) is a highly integrated suite of homology search, template-based modeling, structure prediction, macromolecular docking, biological information incorporation and job management for robust and fast protein–protein docking. With input information for receptor and ligand molecules (either amino acid sequences or Protein Data Bank structures), the server automatically predicts their interaction through a hybrid algorithm of template-based and template-free docking. The HDOCK server distinguishes itself from similar docking servers in its ability to support amino acid sequences as input and a hybrid docking strategy in which experimental information about the protein–protein binding site and small-angle X-ray scattering can be incorporated during the docking and post-docking processes. Moreover, HDOCK also supports protein–RNA/DNA docking with an intrinsic scoring function. The server delivers both template- and docking-based binding models of two molecules and allows for download and interactive visualization. The HDOCK server is user friendly and has processed >30,000 docking jobs since its official release in 2017. The server can normally complete a docking job within 30 min. The HDOCK server is developed for template-based and template-free protein–protein docking, using amino acid sequences or PDB structures as inputs. HDOCK can incorporate SAXS data and can be applied to protein–RNA/DNA docking.

[1]  Lazaros Mavridis,et al.  HexServer: an FFT-based protein docking server powered by graphics processors , 2010, Nucleic Acids Res..

[2]  Feng Ding,et al.  RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures , 2015, RNA.

[3]  Tammy M. K. Cheng,et al.  pyDock: Electrostatics and desolvation for effective scoring of rigid‐body protein–protein docking , 2007, Proteins.

[4]  M. Jette,et al.  Simple Linux Utility for Resource Management , 2009 .

[5]  Xiaoqin Zou,et al.  A knowledge-based scoring function for protein-RNA interactions derived from a statistical mechanics-based iterative method , 2014, Nucleic acids research.

[6]  Rodrigo Lopez,et al.  Clustal W and Clustal X version 2.0 , 2007, Bioinform..

[7]  K. Schweimer,et al.  SuhB is an integral part of the ribosomal antitermination complex and interacts with NusA , 2019, Nucleic acids research.

[8]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[9]  Stephani Joy Y Macalino,et al.  Evolution of In Silico Strategies for Protein-Protein Interaction Drug Discovery , 2018, Molecules.

[10]  J. Janin,et al.  Computer analysis of protein-protein interaction. , 1978, Journal of molecular biology.

[11]  Marc A. Martí-Renom,et al.  Quantifying the relationship between sequence and three-dimensional structure conservation in RNA , 2009, BMC Bioinformatics.

[12]  Zhiping Weng,et al.  ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers , 2014, Bioinform..

[13]  Yang Zhang,et al.  Scoring function for automated assessment of protein structure template quality , 2004, Proteins.

[14]  Sergey Lyskov,et al.  The RosettaDock server for local protein–protein docking , 2008, Nucleic Acids Res..

[15]  Sandor Vajda,et al.  ClusPro: a fully automated algorithm for protein-protein docking , 2004, Nucleic Acids Res..

[16]  Yang Zhang,et al.  RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA , 2019, Bioinform..

[17]  Andrey Tovchigrechko,et al.  GRAMM-X public web server for protein–protein docking , 2006, Nucleic Acids Res..

[18]  Prabhakar Tiwari,et al.  Structural, functional and biological insights into the role of Mycobacterium tuberculosis VapBC11 toxin–antitoxin system: targeting a tRNase to tackle mycobacterial adaptation , 2018, Nucleic acids research.

[19]  Mieczyslaw Torchala,et al.  SwarmDock: a server for flexible protein-protein docking , 2013, Bioinform..

[20]  M. Sternberg,et al.  Modelling protein docking using shape complementarity, electrostatics and biochemical information. , 1997, Journal of molecular biology.

[21]  Greg L. Hura,et al.  X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution. , 2011, Quarterly reviews of biophysics.

[22]  Dima Kozakov,et al.  The ClusPro web server for protein–protein docking , 2017, Nature Protocols.

[23]  Pierre Tufféry,et al.  InterEvDock: a docking server to predict the structure of protein–protein interactions using evolutionary information , 2016, Nucleic Acids Res..

[24]  D. Svergun,et al.  Structural analysis of intrinsically disordered proteins by small-angle X-ray scattering. , 2012, Molecular bioSystems.

[25]  Sheng-You Huang,et al.  Pushing the accuracy limit of shape complementarity for protein-protein docking , 2019, BMC Bioinformatics.

[26]  Chengfei Yan,et al.  Performance of MDockPP in CAPRI rounds 28‐29 and 31‐35 including the prediction of water‐mediated interactions , 2017, Proteins.

[27]  Shengyou Huang,et al.  CHDOCK: a hierarchical docking approach for modeling Cn symmetric homo-oligomeric complexes , 2019, Biophysics Reports.

[28]  Thomas A. Hopf,et al.  Sequence co-evolution gives 3D contacts and structures of protein complexes , 2014, eLife.

[29]  Xiaoqin Zou,et al.  A nonredundant structure dataset for benchmarking protein‐RNA computational docking , 2013, J. Comput. Chem..

[30]  Arne Elofsson,et al.  Assessment of global and local model quality in CASP8 using Pcons and ProQ , 2009, Proteins.

[31]  Dan Li,et al.  HawkDock: a web server to predict and analyze the protein–protein complex based on computational docking and MM/GBSA , 2019, Nucleic Acids Res..

[32]  Martin Zacharias,et al.  SAXS Data Alone can Generate High-Quality Models of Protein-Protein Complexes. , 2016, Structure.

[33]  Carles Pons,et al.  pyDockWEB: a web server for rigid-body protein-protein docking using electrostatics and desolvation scoring , 2013, Bioinform..

[34]  Dima Kozakov,et al.  Sampling and scoring: A marriage made in heaven , 2013, Proteins.

[35]  Laura Pérez-Cano,et al.  A protein‐RNA docking benchmark (II): Extended set from experimental and homology modeling data , 2012, Proteins.

[36]  Zeyu Wen,et al.  Addressing recent docking challenges: A hybrid strategy to integrate template‐based and free protein‐protein docking , 2017, Proteins.

[37]  Andy B. Yoo,et al.  Approved for Public Release; Further Dissemination Unlimited X-ray Pulse Compression Using Strained Crystals X-ray Pulse Compression Using Strained Crystals , 2002 .

[38]  Yang Zhang,et al.  The I-TASSER Suite: protein structure and function prediction , 2014, Nature Methods.

[39]  Eric Westhof,et al.  RNA Structure: Advances and Assessment of 3D Structure Prediction. , 2017, Annual review of biophysics.

[40]  Zhiping Weng,et al.  Protein–protein docking benchmark version 4.0 , 2010, Proteins.

[41]  Xiang-Jun Lu,et al.  Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures , 2019, Nucleic Acids Res..

[42]  Jiahua He,et al.  Challenges and opportunities of automated protein‐protein docking: HDOCK server vs human predictions in CAPRI Rounds 38‐46 , 2020, Proteins.

[43]  Daisuke Kihara,et al.  Protein-protein docking using region-based 3D Zernike descriptors , 2009, BMC Bioinformatics.

[44]  Minkyung Baek,et al.  GalaxyHomomer: a web server for protein homo-oligomer structure prediction from a monomer sequence or structure , 2017, Nucleic Acids Res..

[45]  I. Vakser,et al.  Evaluation of GRAMM low‐resolution docking methodology on the hemagglutinin‐antibody complex , 1997, Proteins.

[46]  Sheng-You Huang,et al.  HSYMDOCK: a docking web server for predicting the structure of protein homo-oligomers with Cn or Dn symmetry , 2018, Nucleic Acids Res..

[47]  M. Garber,et al.  Fab Fragment of VHH-Based Antibody Netakimab: Crystal Structure and Modeling Interaction with Cytokine IL-17A , 2019 .

[48]  Xiaoqin Zou,et al.  MDockPP: A hierarchical approach for protein‐protein docking and its application to CAPRI rounds 15–19 , 2010, Proteins.

[49]  Alexandre M. J. J. Bonvin,et al.  A protein–DNA docking benchmark , 2008, Nucleic acids research.

[50]  A. Sali,et al.  Protein Structure Prediction and Structural Genomics , 2001, Science.

[51]  Sandor Vajda,et al.  CAPRI: A Critical Assessment of PRedicted Interactions , 2003, Proteins.

[52]  A. Sali,et al.  Comparative protein structure modeling of genes and genomes. , 2000, Annual review of biophysics and biomolecular structure.

[53]  Holger Gohlke,et al.  The Amber biomolecular simulation programs , 2005, J. Comput. Chem..

[54]  Jill Trewhella,et al.  Small‐angle scattering for structural biology—Expanding the frontier while avoiding the pitfalls , 2010, Protein science : a publication of the Protein Society.

[55]  Sameer Velankar,et al.  Modeling protein‐protein, protein‐peptide, and protein‐oligosaccharide complexes: CAPRI 7th edition , 2019, Proteins.

[56]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[57]  Elodie Laine,et al.  Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment , 2019, Proteins.

[58]  A. Wilm,et al.  A benchmark of multiple sequence alignment programs upon structural RNAs , 2005, Nucleic acids research.

[59]  Isaure Chauvot de Beauchêne,et al.  A web interface for easy flexible protein-protein docking with ATTRACT. , 2015, Biophysical journal.

[60]  Dmitri I. Svergun,et al.  SASBDB, a repository for biological small-angle scattering data , 2014, Nucleic Acids Res..

[61]  Andreas Prlic,et al.  NGL viewer: web‐based molecular graphics for large complexes , 2018, Bioinform..

[62]  Ilya A Vakser,et al.  Protein-protein docking: from interaction to interactome. , 2014, Biophysical journal.

[63]  Cole H. Christie,et al.  Protein Data Bank: the single global archive for 3D macromolecular structure data , 2018, Nucleic Acids Res..

[64]  A. Elofsson,et al.  Can correct protein models be identified? , 2003, Protein science : a publication of the Protein Society.

[65]  Peter F. Stadler,et al.  ViennaRNA Package 2.0 , 2011, Algorithms for Molecular Biology.

[66]  C. Dominguez,et al.  HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. , 2003, Journal of the American Chemical Society.

[67]  S. Wodak,et al.  Assessment of blind predictions of protein–protein interactions: Current status of docking methods , 2003, Proteins.

[68]  Sheng-You Huang,et al.  A non-redundant benchmark for symmetric protein docking , 2019, Big Data Min. Anal..

[69]  Michael J. E. Sternberg,et al.  3D-Garden: a system for modelling protein-protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm , 2008, Bioinform..

[70]  Dima Kozakov,et al.  What method to use for protein-protein docking? , 2019, Current opinion in structural biology.

[71]  Yang Zhang,et al.  I-TASSER: a unified platform for automated protein structure and function prediction , 2010, Nature Protocols.

[72]  Janusz M. Bujnicki,et al.  NPDock: a web server for protein–nucleic acid docking , 2015, Nucleic Acids Res..

[73]  Jian Wang,et al.  3dRNAscore: a distance and torsion angle dependent evaluation function of 3D RNA structures , 2015, Nucleic acids research.

[74]  Dmitri I Svergun,et al.  Preparing monodisperse macromolecular samples for successful biological small-angle X-ray and neutron-scattering experiments , 2016, Nature Protocols.

[75]  Andrej Sali,et al.  Macromolecular docking restrained by a small angle X-ray scattering profile. , 2011, Journal of structural biology.

[76]  Sheng-You Huang,et al.  Search strategies and evaluation in protein-protein docking: principles, advances and challenges. , 2014, Drug discovery today.

[77]  Taras Dauzhenka,et al.  Dockground: A comprehensive data resource for modeling of protein complexes , 2018, Protein science : a publication of the Protein Society.

[78]  Mushtaq Ahmed,et al.  The molecular link between tyrosol binding to tri6 transcriptional regulator and downregulation of trichothecene biosynthesis. , 2019, Biochimie.

[79]  J. Bujnicki,et al.  ModeRNA: a tool for comparative modeling of RNA 3D structure , 2011, Nucleic acids research.

[80]  Yi Xiao,et al.  Using 3dRNA for RNA 3‐D Structure Prediction and Evaluation , 2017, Current protocols in bioinformatics.

[81]  J. Skolnick,et al.  TM-align: a protein structure alignment algorithm based on the TM-score , 2005, Nucleic acids research.

[82]  Ruth Nussinov,et al.  PatchDock and SymmDock: servers for rigid and symmetric docking , 2005, Nucleic Acids Res..

[83]  Chengfei Yan,et al.  Inclusion of the orientational entropic effect and low‐resolution experimental information for protein–protein docking in Critical Assessment of PRedicted Interactions (CAPRI) , 2013, Proteins.

[84]  A. Bonvin,et al.  The HADDOCK web server for data-driven biomolecular docking , 2010, Nature Protocols.

[85]  E. Katchalski‐Katzir,et al.  Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[86]  Yang Zhang,et al.  I-TASSER server: new development for protein structure and function predictions , 2015, Nucleic Acids Res..

[87]  D. Lipman,et al.  Improved tools for biological sequence comparison. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[88]  Yang Zhang,et al.  How significant is a protein structure similarity with TM-score = 0.5? , 2010, Bioinform..

[89]  Dmitri I. Svergun,et al.  pyDockSAXS: protein–protein complex structure by SAXS and computational docking , 2015, Nucleic Acids Res..

[90]  Anne Martel,et al.  The accurate assessment of small-angle X-ray scattering data , 2015, Acta crystallographica. Section D, Biological crystallography.

[91]  Markus Schneider,et al.  Chemical Cross-Linking Enables Drafting ClpXP Proximity Maps and Taking Snapshots of In Situ Interaction Networks. , 2019, Cell chemical biology.

[92]  Jian Wang,et al.  Optimization of RNA 3D structure prediction using evolutionary restraints of nucleotide–nucleotide interactions from direct coupling analysis , 2017, Nucleic acids research.

[93]  Ranjit Prasad Bahadur,et al.  A non‐redundant protein–RNA docking benchmark version 2.0 , 2017, Proteins.

[94]  A. Tramontano,et al.  Critical assessment of methods of protein structure prediction (CASP)—round IX , 2011, Proteins.

[95]  A. Biegert,et al.  HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment , 2011, Nature Methods.

[96]  Xiaoqin Zou,et al.  An iterative knowledge‐based scoring function for protein–protein recognition , 2008, Proteins.

[97]  P. V. Konarev,et al.  ATSAS 2.8: a comprehensive data analysis suite for small-angle scattering from macromolecular solutions , 2017, Journal of applied crystallography.

[98]  Sheng-You Huang,et al.  Protein-Protein Docking with Improved Shape Complementarity , 2018, ICIC.

[99]  Pei Zhou,et al.  HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy , 2017, Nucleic Acids Res..

[100]  Jun Hu,et al.  A method for aligning RNA secondary structures and its application to RNA motif detection , 2005, BMC Bioinformatics.

[101]  Sameer Velankar,et al.  The challenge of modeling protein assemblies: the CASP12‐CAPRI experiment , 2018, Proteins.

[102]  Sheng-You Huang,et al.  Exploring the potential of global protein-protein docking: an overview and critical assessment of current programs for automatic ab initio docking. , 2015, Drug discovery today.

[103]  Daisuke Kihara,et al.  Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: A CASP‐CAPRI experiment , 2016, Proteins.

[104]  Janusz M Bujnicki,et al.  Bioinformatics Tools and Benchmarks for Computational Docking and 3D Structure Prediction of RNA-Protein Complexes , 2018, Genes.

[105]  Yangyu Huang,et al.  Automated and fast building of three-dimensional RNA structures , 2012, Scientific Reports.

[106]  Qing Wu,et al.  ComplexContact: a web server for inter-protein contact prediction using deep learning , 2018, Nucleic Acids Res..

[107]  Katarzyna J Purzycka,et al.  RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. , 2017, RNA.

[108]  G C P van Zundert,et al.  The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes. , 2016, Journal of molecular biology.

[109]  Torsten Schwede,et al.  Critical assessment of methods of protein structure prediction (CASP)—Round XIII , 2019, Proteins.