Structural modeling of protein complexes: Current capabilities and challenges

VoroMQA web server for assessing three-dimensional structures of proteins and protein complexes

(2019) Kliment Olechnovič et al.   NUCLEIC ACIDS RESEARCH

A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core

(2018) Lukas Zimmermann et al.   JOURNAL OF MOLECULAR BIOLOGY

HMMER web server: 2018 update

(2018) Simon C Potter et al.   NUCLEIC ACIDS RESEARCH

Automated evaluation of quaternary structures from protein crystals

(2018) Spencer Bliven et al.   PLoS Computational Biology

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

Automatic structure prediction of oligomeric assemblies using Robetta in CASP12

(2017) Hahnbeom Park et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Modeling of protein complexes in CAPRI Round 37 using template-based approach combined with model selection

(2017) Justas Dapkūnas et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Template-based quaternary structure prediction of proteins using enhanced profile-profile alignments

(2017) Tsukasa Nakamura et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

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

Assessment of protein assembly prediction in CASP12

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

InterPred: A pipeline to identify and model protein-protein interactions

(2017) Claudio Mirabello et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

VoroMQA: Assessment of protein structure quality using interatomic contact areas

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

Critical assessment of methods of protein structure prediction (CASP)-Round XII

(2017) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Evaluation of the template-based modeling in CASP12

(2017) Andriy Kryshtafovych 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

PPI4DOCK: large scale assessment of the use of homology models in free docking over more than 1000 realistic targets

(2016) Jinchao Yu et al.   BIOINFORMATICS

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

(2016) Ozlem Keskin et al.   CHEMICAL REVIEWS

Lessons from (co-)evolution in the docking of proteins and peptides for CAPRI Rounds 28-35

(2016) Jinchao Yu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Modeling complexes of modeled proteins

(2016) Ivan Anishchenko et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

Modeling protein-protein and protein-peptide complexes: CAPRI 6th edition

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

Spherical polar Fourier assembly of protein complexes with arbitrary point group symmetry

(2016) David W. Ritchie et al.   JOURNAL OF APPLIED CRYSTALLOGRAPHY

Voronota: A fast and reliable tool for computing the vertices of the Voronoi diagram of atomic balls

(2014) Kliment Olechnovič et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Assessing the Applicability of Template-Based Protein Docking in the Twilight Zone

(2014) Jacopo Negroni et al.   STRUCTURE

Structure-Based Characterization of Multiprotein Complexes

(2014) Markus Wiederstein et al.   STRUCTURE

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

InterEvScore: a novel coarse-grained interface scoring function using a multi-body statistical potential coupled to evolution

(2013) Jessica Andreani et al.   BIOINFORMATICS

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

(2013) Valerio Mariani et al.   BIOINFORMATICS

pyDockWEB: a web server for rigid-body protein–protein docking using electrostatics and desolvation scoring

(2013) Brian Jiménez-García et al.   BIOINFORMATICS

Template-based structure modeling of protein–protein interactions

(2013) Andras Szilagyi et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Long tail fibres of the novel broad-host-range T-even bacteriophage S16 specifically recognizeSalmonellaOmpC

(2013) Roger Marti et al.   MOLECULAR MICROBIOLOGY

CAD-score: A new contact area difference-based function for evaluation of protein structural models

(2013) Kliment Olechnovič et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Alternative Protein-Protein Interfaces Are Frequent Exceptions

(2012) Tobias Hamp et al.   PLoS Computational Biology

Atomic-Level Protein Structure Refinement Using Fragment-Guided Molecular Dynamics Conformation Sampling

(2011) Jian Zhang et al.   STRUCTURE

Docking by structural similarity at protein-protein interfaces

(2010) Rohita Sinha et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Statistical Analysis of Interface Similarity in Crystals of Homologous Proteins

(2008) Qifang Xu et al.   JOURNAL OF MOLECULAR BIOLOGY