ComplexQA: a deep graph learning approach for protein complex structure assessment

A gated graph transformer for protein complex structure quality assessment and its performance in CASP15

(2023) Xiao Chen et al.   BIOINFORMATICS

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

(2022) Linyuan Guo et al.   BIOINFORMATICS

Artificial intelligence advances for de novo molecular structure modeling in cryo‐electron microscopy

(2021) Dong Si et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

ZoomQA: residue-level protein model accuracy estimation with machine learning on sequential and 3D structural features

(2021) Kyle Hippe et al.   BRIEFINGS IN BIOINFORMATICS

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

GraphQA: Protein Model Quality Assessment using Graph Convolutional Networks

(2020) Federico Baldassarre et al.   BIOINFORMATICS

DeepTracer for fast de novo cryo-EM protein structure modeling and special studies on CoV-related complexes

(2020) Jonas Pfab et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein tertiary structure modeling driven by deep learning and contact distance prediction in CASP13

(2019) Jie Hou et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Coupling Molecular Dynamics and Deep Learning to Mine Protein Conformational Space

(2019) Matteo T. Degiacomi   STRUCTURE

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

(2019) Cunliang Geng et al.   BIOINFORMATICS

Protein Docking Model Evaluation by 3D Deep Convolutional Neural Networks

(2019) Xiao Wang et al.   BIOINFORMATICS

Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning

(2019) P. Gainza et al.   NATURE METHODS

HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy

(2017) Yumeng Yan et al.   NUCLEIC ACIDS RESEARCH

VoroMQA: Assessment of protein structure quality using interatomic contact areas

(2017) Kliment Olechnovič et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Finding correct protein–protein docking models using ProQDock

(2016) Sankar Basu et al.   BIOINFORMATICS

DeepQA: improving the estimation of single protein model quality with deep belief networks

(2016) Renzhi Cao et al.   BMC BIOINFORMATICS

InterEvDock: a docking server to predict the structure of protein–protein interactions using evolutionary information

(2016) Jinchao Yu et al.   NUCLEIC ACIDS RESEARCH

DockQ: A Quality Measure for Protein-Protein Docking Models

(2016) Sankar Basu et al.   PLoS One

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

(2016) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

Structural templates for comparative protein docking

(2015) Ivan Anishchenko et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers

(2014) B. G. Pierce et al.   BIOINFORMATICS

SMOQ: a tool for predicting the absolute residue-specific quality of a single protein model with support vector machines

(2014) Renzhi Cao et al.   BMC BIOINFORMATICS

Score_set: A CAPRI benchmark for scoring protein complexes

(2014) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests

(2013) Valerio Mariani et al.   BIOINFORMATICS

SwarmDock: a server for flexible protein–protein docking

(2013) Mieczyslaw Torchala et al.   BIOINFORMATICS

Interactome3D: adding structural details to protein networks

(2012) Roberto Mosca et al.   NATURE METHODS

GOAP: A Generalized Orientation-Dependent, All-Atom Statistical Potential for Protein Structure Prediction

(2011) Hongyi Zhou et al.   BIOPHYSICAL JOURNAL

Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM

(2011) Nurcan Tuncbag et al.   Nature Protocols

Accelerating Protein Docking in ZDOCK Using an Advanced 3D Convolution Library

(2011) Brian G. Pierce et al.   PLoS One

Engineering hybrid nanotube wires for high-power biofuel cellspace

(2010) Feng Gao et al.   Nature Communications

DOCKGROUND protein-protein docking decoy set

(2008) S. Liu et al.   BIOINFORMATICS

The RosettaDock server for local protein-protein docking

(2008) S. Lyskov et al.   NUCLEIC ACIDS RESEARCH

A combination of rescoring and refinement significantly improves protein docking performance

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