What method to use for protein-protein docking?

A number of well-established servers perform 'free' docking of proteins of known structures. In contrast, template-based docking can start from sequences if structures are available for complexes that are homologous to the target. On the basis of the results of the CAPRI-CASP structure prediction experiments, template-based methods yield more accurate predictions if good templates can be found, but generally fail without such templates. However, free global docking, or focused docking around even poor quality template-based models, can still generate acceptable docked structures in these cases. In accordance with the analysis of a benchmark set, free docking of heterodimers yields acceptable or better predictions in the top 10 models for around 40% of structures. However, it is likely that a combination of template-based and free docking methods can perform better for targets that have template structures available. Another way of improving the reliability of predictions is adding experimental information as restraints, an option built into several docking servers.

[1]  Carles Pons,et al.  Optimization of pyDock for the new CAPRI challenges: Docking of homology‐based models, domain–domain assembly and protein‐RNA binding , 2010, Proteins.

[2]  Z. Weng,et al.  Protein–protein docking benchmark version 3.0 , 2008, Proteins.

[3]  Ruth Nussinov,et al.  Computing the Dynamic Supramolecular Structural Proteome , 2017, PLoS Comput. Biol..

[4]  G C P van Zundert,et al.  Sense and simplicity in HADDOCK scoring: Lessons from CASP‐CAPRI round 1 , 2016, Proteins.

[5]  Zhiping Weng,et al.  IRaPPA: information retrieval based integration of biophysical models for protein assembly selection , 2017, Bioinform..

[6]  A. Bonvin,et al.  On the usefulness of ion-mobility mass spectrometry and SAXS data in scoring docking decoys. , 2013, Acta crystallographica. Section D, Biological crystallography.

[7]  Juan Fernández-Recio,et al.  pyDock scoring for the new modeling challenges in docking: Protein–peptide, homo‐multimers, and domain–domain interactions , 2017, Proteins.

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

[9]  Zhengwei Zhu,et al.  Templates are available to model nearly all complexes of structurally characterized proteins , 2012, Proceedings of the National Academy of Sciences.

[10]  Raphael A. G. Chaleil,et al.  Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2. , 2015, Journal of molecular biology.

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

[12]  Bing Xia,et al.  Accounting for pairwise distance restraints in FFT-based protein-protein docking , 2016, Bioinform..

[13]  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..

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

[15]  Z. Weng,et al.  Protein–protein docking benchmark 2.0: An update , 2005, Proteins.

[16]  Paul A Bates,et al.  Flexible Protein-Protein Docking with SwarmDock. , 2018, Methods in molecular biology.

[17]  M J Sternberg,et al.  Use of pair potentials across protein interfaces in screening predicted docked complexes , 1999, Proteins.

[18]  Dima Kozakov,et al.  New additions to the ClusPro server motivated by CAPRI , 2017, Proteins.

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

[20]  S. Wodak,et al.  Modeling protein–protein and protein–peptide complexes: CAPRI 6th edition , 2017, Proteins.

[21]  Dima Kozakov,et al.  ClusPro FMFT-SAXS: Ultra-fast Filtering Using Small-Angle X-ray Scattering Data in Protein Docking. , 2018, Journal of molecular biology.

[22]  Genki Terashi,et al.  Human and server docking prediction for CAPRI round 30‐35 using LZerD with combined scoring functions , 2017, Proteins.

[23]  Johannes Söding,et al.  The HHpred interactive server for protein homology detection and structure prediction , 2005, Nucleic Acids Res..

[24]  P. Aloy,et al.  Interactome3D: adding structural details to protein networks , 2013, Nature Methods.

[25]  Luhua Lai,et al.  SDOCK: A global protein‐protein docking program using stepwise force‐field potentials , 2011, J. Comput. Chem..

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

[27]  Stephen R. Comeau,et al.  PIPER: An FFT‐based protein docking program with pairwise potentials , 2006, Proteins.

[28]  Alexandre M. J. J. Bonvin,et al.  CPORT: A Consensus Interface Predictor and Its Performance in Prediction-Driven Docking with HADDOCK , 2011, PloS one.

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

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

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

[32]  Pierre Tufféry,et al.  InterEvDock2: an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs , 2018, Nucleic Acids Res..

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

[34]  Dima Kozakov,et al.  Application of asymmetric statistical potentials to antibody-protein docking , 2012, Bioinform..

[35]  Juan Fernández-Recio,et al.  CCharPPI web server: computational characterization of protein-protein interactions from structure , 2015, Bioinform..

[36]  Björn Wallner,et al.  DockQ: A Quality Measure for Protein-Protein Docking Models , 2016, PloS one.

[37]  Zhiping Weng,et al.  Integrating cross-linking experiments with ab initio protein-protein docking , 2018, bioRxiv.

[38]  Bing Xia,et al.  Accounting for observed small angle X‐ray scattering profile in the protein–protein docking server cluspro , 2015, J. Comput. Chem..

[39]  Christopher R. Corbeil,et al.  ProPOSE: Direct Exhaustive Protein-Protein Docking with Side Chain Flexibility. , 2018, Journal of chemical theory and computation.

[40]  Ben M. Webb,et al.  Comparative Protein Structure Modeling Using MODELLER , 2007, Current protocols in protein science.

[41]  Zhiping Weng,et al.  A protein–protein docking benchmark , 2003, Proteins.

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