TRScore: a 3D RepVGG-based scoring method for ranking protein docking models

Accurate prediction of inter-protein residue–residue contacts for homo-oligomeric protein complexes

(2021) Yumeng Yan et al.   BRIEFINGS IN BIOINFORMATICS

Large-scale discovery of protein interactions at residue resolution using co-evolution calculated from genomic sequences

(2021) Anna G. Green et al.   Nature Communications

Structure-aware protein solubility prediction from sequence through graph convolutional network and predicted contact map

(2021) Jianwen Chen et al.   Journal of Cheminformatics

Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment

(2021) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Improved protein structure prediction using potentials from deep learning

(2020) Andrew W. Senior et al.   NATURE

A knowledge-based scoring function to assess quaternary associations of proteins

(2020) Abhilesh S Dhawanjewar et al.   BIOINFORMATICS

The HDOCK server for integrated protein–protein docking

(2020) Yumeng Yan et al.   Nature Protocols

aPRBind: protein-RNA interface prediction by combining sequence and I-TASSER model-based structural features learned with convolutional neural networks

(2020) Yang Liu et al.   BIOINFORMATICS

What method to use for protein–protein docking?

(2019) Kathryn A Porter et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Asymmetry in catalysis by Thermotoga maritima membrane-bound pyrophosphatase demonstrated by a nonphosphorus allosteric inhibitor

(2019) Keni Vidilaseris et al.   Science Advances

iScore: A novel graph kernel-based function for scoring protein-protein docking models

(2019) Cunliang Geng et al.   BIOINFORMATICS

Protein contact prediction using metagenome sequence data and residual neural networks

(2019) Qi Wu et al.   BIOINFORMATICS

Protein Docking Model Evaluation by 3D Deep Convolutional Neural Networks

(2019) Xiao Wang et al.   BIOINFORMATICS

Attention mechanism enhanced LSTM with residual architecture and its application for protein-protein interaction residue pairs prediction

(2019) Jiale Liu et al.   BMC BIOINFORMATICS

Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment

(2019) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning

(2019) P. Gainza et al.   NATURE METHODS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Inter-residue, inter-protein and inter-family coevolution: bridging the scales

(2018) Hendrik Szurmant et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

KDEEP: Protein–Ligand Absolute Binding Affinity Prediction via 3D-Convolutional Neural Networks

(2018) José Jiménez et al.   Journal of Chemical Information and Modeling

InterEvDock2: an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs

(2018) Chloé Quignot et al.   NUCLEIC ACIDS RESEARCH

Cryo-EM structure of the yeast respiratory supercomplex

(2018) Sorbhi Rathore et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Protein–Ligand Scoring with Convolutional Neural Networks

(2017) Matthew Ragoza et al.   Journal of Chemical Information and Modeling

The ClusPro web server for protein–protein docking

(2017) Dima Kozakov et al.   Nature Protocols

The challenge of modeling protein assemblies: the CASP12-CAPRI experiment

(2017) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Finding correct protein–protein docking models using ProQDock

(2016) Sankar Basu et al.   BIOINFORMATICS

Current Experimental Methods for Characterizing Protein-Protein Interactions

(2016) Mi Zhou et al.   ChemMedChem

Small molecules, big targets: drug discovery faces the protein–protein interaction challenge

(2016) Duncan E. Scott et al.   NATURE REVIEWS DRUG DISCOVERY

DockQ: A Quality Measure for Protein-Protein Docking Models

(2016) Sankar Basu et al.   PLoS One

Protein–protein docking by fast generalized Fourier transforms on 5D rotational manifolds

(2016) Dzmitry Padhorny et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Updates to the Integrated Protein–Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2

(2015) Thom Vreven et al.   JOURNAL OF MOLECULAR BIOLOGY

Bacterial protein networks: properties and functions

(2015) Athanasios Typas et al.   NATURE REVIEWS MICROBIOLOGY

Search strategies and evaluation in protein–protein docking: principles, advances and challenges

(2014) Sheng-You Huang   DRUG DISCOVERY TODAY

Relaxation of backbone bond geometry improves protein energy landscape modeling

(2013) Patrick Conway et al.   PROTEIN SCIENCE

Combining Statistical Potentials with Dynamics-Based Entropies Improves Selection from Protein Decoys and Docking Poses

(2012) Michael T. Zimmermann et al.   JOURNAL OF PHYSICAL CHEMISTRY B

DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking

(2011) Shiyong Liu et al.   BMC BIOINFORMATICS

Integrating atom-based and residue-based scoring functions for protein-protein docking

(2011) Thom Vreven et al.   PROTEIN SCIENCE

SwarmDock and the Use of Normal Modes in Protein-Protein Docking

(2010) Iain H. Moal et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Protein-protein docking benchmark version 4.0

(2010) Howook Hwang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

DOCKGROUND protein-protein docking decoy set

(2008) S. Liu et al.   BIOINFORMATICS

A combination of rescoring and refinement significantly improves protein docking performance

(2008) Brian Pierce et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

An iterative knowledge-based scoring function for protein-protein recognition

(2008) Sheng-You Huang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS