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

VoroMQA: Assessment of protein structure quality using interatomic contact areas

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

Protein structure determination using metagenome sequence data

(2017) Sergey Ovchinnikov et al.   SCIENCE

Structured States of Disordered Proteins from Genomic Sequences

(2016) Agnes Toth-Petroczy et al.   CELL

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

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

Evaluation of free modeling targets in CASP11 and ROLL

(2016) Lisa N. Kinch 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

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

(2016) Sergey Ovchinnikov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2015) Li C. Xue et al.   FEBS LETTERS

Landscape of Intertwined Associations in Multi-Domain Homo-Oligomeric Proteins

(2015) Stephen S. MacKinnon et al.   JOURNAL OF MOLECULAR BIOLOGY

PDBFlex: exploring flexibility in protein structures

(2015) Thomas Hrabe et al.   NUCLEIC ACIDS RESEARCH

MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins

(2014) David T. Jones et al.   BIOINFORMATICS

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

(2014) Jacopo Negroni et al.   STRUCTURE

A PDB-wide, evolution-based assessment of protein-protein interfaces

(2014) Kumaran Baskaran et al.   BMC STRUCTURAL BIOLOGY

Template-based structure modeling of protein–protein interactions

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

Trendspotting in the Protein Data Bank

(2013) Helen M. Berman et al.   FEBS LETTERS

Coevolutionary signals across protein lineages help capture multiple protein conformations

(2013) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Blind prediction of interfacial water positions in CAPRI

(2013) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

(2013) Rocco Moretti et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Docking, scoring, and affinity prediction in CAPRI

(2013) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Integrative Structural Biology

(2013) A. B. Ward et al.   SCIENCE

Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing

(2012) Timothy A Whitehead et al.   NATURE BIOTECHNOLOGY

Protein structure prediction from sequence variation

(2012) Debora S Marks et al.   NATURE BIOTECHNOLOGY

Templates are available to model nearly all complexes of structurally characterized proteins

(2012) P. J. Kundrotas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) Hongyi Zhou et al.   BIOPHYSICAL JOURNAL

Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology

(2011) Sarel J. Fleishman et al.   JOURNAL OF MOLECULAR BIOLOGY

Statistical mechanics-based method to extract atomic distance-dependent potentials from protein structures

(2011) Sheng-You Huang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Subunit Interfaces of Weakly Associated Homodimeric Proteins

(2010) Sucharita Dey et al.   JOURNAL OF MOLECULAR BIOLOGY

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

Docking and scoring protein interactions: CAPRI 2009

(2010) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Blind predictions of protein interfaces by docking calculations in CAPRI

(2010) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Convergence and combination of methods in protein–protein docking

(2009) Sandor Vajda et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Fast and accurate automatic structure prediction with HHpred

(2009) Andrea Hildebrand et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Recent Progress and Future Directions in Protein-Protein Docking

(2008) David Ritchie   CURRENT PROTEIN & PEPTIDE SCIENCE

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

(2008) Sjoerd de Vries et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Protein networks in disease

(2008) T. Ideker et al.   GENOME RESEARCH

Statistical Analysis of Interface Similarity in Crystals of Homologous Proteins

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

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

(2002) Hongyi Zhou et al.   PROTEIN SCIENCE