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Strengths and weaknesses of data‐driven docking in critical assessment of prediction of interactions

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Prediction of interface residues in protein–protein complexes by a consensus neural network method: Test against NMR data

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Docking to single‐domain and multiple‐domain proteins: Old and new challenges

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Data‐driven docking: HADDOCK's adventures in CAPRI

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WHISCY: What information does surface conservation yield? Application to data‐driven docking

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PIER: Protein interface recognition for structural proteomics

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Prediction‐based fingerprints of protein–protein interactions

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Prediction of RNA binding sites in a protein using SVM and PSSM profile

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HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets

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Self-association of TPR domains: Lessons learned from a designed, consensus-based TPR oligomer

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A multiple‐start Monte Carlo docking method

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Comparative Protein Modelling by Satisfaction of Spatial Restraints

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Specificity in protein-protein interactions: the structural basis for dual recognition in endonuclease colicin-immunity protein complexes

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RISP: A web-based server for prediction of RNA-binding sites in proteins

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Identification of Protein–Protein Interaction Sites from Docking Energy Landscapes

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ProMate: A Structure Based Prediction Program to Identify the Location of Protein–Protein Binding Sites

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Prediction of Multimolecular Assemblies by Multiple Docking

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Structural and Mutational Analyses of the Interaction between the Barley α-Amylase/Subtilisin Inhibitor and the Subtilisin Savinase Reveal a Novel Mode of Inhibition

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Convergence and combination of methods in protein–protein docking

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Structure of the Yeast tRNA m7G Methylation Complex

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Antigenic determinants and reactive sites of a trypsin/chymotrypsin double-headed inhibitor from horse gram (Dolichos biflorus)

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Design of Stable α-Helical Arrays from an Idealized TPR Motif

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Barley α-amylase bound to its endogenous protein inhibitor BASI: crystal structure of the complex at 1.9 å resolution

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The crystal structure of the DNase domain of colicin E7 in complex with its inhibitor Im7 protein

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Structural and Functional Versatility of the FHA Domain in DNA-Damage Signaling by the Tumor Suppressor Kinase Chk2

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Episelection: Novel Ki .apprx. Nanomolar Inhibitors of Serine Proteases Selected by Binding or Chemistry on an Enzyme Surface

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Dual Recognition and the Role of Specificity-Determining Residues in Colicin E9 DNase−Immunity Protein Interactions

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The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin

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HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information

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Structure Determination of Protein−Protein Complexes Using NMR Chemical Shifts: Case of an Endonuclease Colicin−Immunity Protein Complex

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The structural basis of Arf effector specificity: the crystal structure of ARF6 in a complex with JIP4

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The HADDOCK web server for data-driven biomolecular docking

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Structural basis for Rab11-dependent membrane recruitment of a family of Rab11-interacting protein 3 (FIP3)/Arfophilin-1

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The structural and energetic basis for high selectivity in a high-affinity protein-protein interaction

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The Ternary Structure of the Double-headed Arrowhead Protease Inhibitor API-A Complexed with Two Trypsins Reveals a Novel Reactive Site Conformation

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Binding of Rac1, Rnd1, and RhoD to a Novel Rho GTPase Interaction Motif Destabilizes Dimerization of the Plexin-B1 Effector Domain

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Building Macromolecular Assemblies by Information-driven Docking

inferredcites →https://doi.org/10.1093/emboj/21.6.1255openalex-snapshot

Conserved segments 1A and 2B of the intermediate filament dimer: their atomic structures and role in filament assembly

inferredcites →https://doi.org/10.1093/nar/gkl454openalex-snapshot

Protein binding site prediction using an empirical scoring function

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RNABindR: a server for analyzing and predicting RNA-binding sites in proteins

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Structure and stability of designed TPR protein superhelices: unusual crystal packing and implications for natural TPR proteins

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Macromolecular docking of a three‐body system: The recognition of human growth hormone by its receptor

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Modeling of loops in protein structures

inferredcites →https://doi.org/10.1111/j.1742-4658.2004.04473.xopenalex-snapshot

Data‐driven docking for the study of biomolecular complexes

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X-Ray Structure of the GCN4 Leucine Zipper, a Two-Stranded, Parallel Coiled Coil

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Data-driven Docking: Using External Information to Spark the Biomolecular Rendez-vous

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I-TASSER server for protein 3D structure prediction

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SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models

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Recent Progress and Future Directions in Protein-Protein Docking

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How Proteins Get in Touch: Interface Prediction in the Study of Biomolecular Complexes

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Clustering biomolecular complexes by residue contacts similarity

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Structural models of DYNLL1 with interacting partners: African swine fever virus protein p54 and postsynaptic scaffolding protein gephyrin

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Computational prediction of protein interfaces: A review of data driven methods

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Structural and functional insights on folate receptor α (FRα) by homology modeling, ligand docking and molecular dynamics

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Computational methods for prediction of protein–RNA interactions

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NMR approaches for structural analysis of multidomain proteins and complexes in solution

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Integrative Modeling of Biomolecular Complexes: HADDOCKing with Cryo-Electron Microscopy Data

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The T-Cell Receptor Can Bind to the Peptide-Bound Major Histocompatibility Complex and Uncomplexed β2-Microglobulin through Distinct Binding Sites

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Modeling of the Water Network at Protein–RNA Interfaces

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