Protein oligomer modeling guided by predicted interchain contacts in CASP14

Improved protein structure refinement guided by deep learning based accuracy estimation

(2021) Naozumi Hiranuma et al.   Nature Communications

Improved protein structure prediction using potentials from deep learning

(2020) Andrew W. Senior et al.   NATURE

Improved protein structure prediction using predicted interresidue orientations

(2020) Jianyi Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Flexible Backbone Assembly and Refinement of Symmetrical Homomeric Complexes

(2019) Shourya S. Roy Burman et al.   STRUCTURE

HH-suite3 for fast remote homology detection and deep protein annotation

(2019) Martin Steinegger et al.   BMC BIOINFORMATICS

Distance-based protein folding powered by deep learning

(2019) Jinbo Xu   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assessment of protein assembly prediction in CASP13

(2019) Dmytro Guzenko et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Prediction of protein oligomer structures using GALAXY in CASP13

(2019) Minkyung Baek et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Deep learning extends de novo protein modelling coverage of genomes using iteratively predicted structural constraints

(2019) Joe G. Greener et al.   Nature Communications

Efficient flexible backbone protein–protein docking for challenging targets

(2018) Nicholas A Marze et al.   BIOINFORMATICS

ComplexContact: a web server for inter-protein contact prediction using deep learning

(2018) Hong Zeng et al.   NUCLEIC ACIDS RESEARCH

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

GalaxyHomomer: a web server for protein homo-oligomer structure prediction from a monomer sequence or structure

(2017) Minkyung Baek et al.   NUCLEIC ACIDS RESEARCH

Assessment of protein assembly prediction in CASP12

(2017) Aleix Lafita et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology

(2017) Martino Bertoni et al.   Scientific Reports

Predicting Protein–Protein Interactions from the Molecular to the Proteome Level

(2016) Ozlem Keskin et al.   CHEMICAL REVIEWS

Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules

(2016) Hahnbeom Park et al.   Journal of Chemical Theory and Computation

Uniclust databases of clustered and deeply annotated protein sequences and alignments

(2016) Milot Mirdita et al.   NUCLEIC ACIDS RESEARCH

IMG/M: integrated genome and metagenome comparative data analysis system

(2016) I-Min A. Chen et al.   NUCLEIC ACIDS RESEARCH

Improved de novo structure prediction in CASP11 by incorporating coevolution information into Rosetta

(2016) Sergey Ovchinnikov 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

Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information

(2014) Sergey Ovchinnikov et al.   eLife

Sequence co-evolution gives 3D contacts and structures of protein complexes

(2014) Thomas A Hopf et al.   eLife

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

(2013) Valerio Mariani et al.   BIOINFORMATICS

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era

(2013) H. Kamisetty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Relaxation of backbone bond geometry improves protein energy landscape modeling

(2013) Patrick Conway et al.   PROTEIN SCIENCE

High-Resolution Comparative Modeling with RosettaCM

(2013) Yifan Song et al.   STRUCTURE

PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta

(2010) S. Chaudhury et al.   BIOINFORMATICS

Learning generative models for protein fold families

(2010) Sivaraman Balakrishnan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming

(2009) Srayanta Mukherjee et al.   NUCLEIC ACIDS RESEARCH

Simultaneous prediction of protein folding and docking at high resolution

(2009) Rhiju Das et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA