Understanding the fabric of protein crystals: computational classification of biological interfaces and crystal contacts

Functional roles of the hexamer organization of plant glutamate decarboxylase

(2015) Alessandra Astegno et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Covariation Is a Poor Measure of Molecular Coevolution

(2015) David Talavera et al.   MOLECULAR BIOLOGY AND EVOLUTION

Cryo-EM: A Unique Tool for the Visualization of Macromolecular Complexity

(2015) Eva Nogales et al.   MOLECULAR CELL

Stock-based detection of protein oligomeric states in jsPISA

(2015) Eugene Krissinel   NUCLEIC ACIDS RESEARCH

Simulation of protein association: Kinetic pathways towards crystal contacts

(2015) Aaron Taudt et al.   PHYSICAL REVIEW E

2.2 A resolution cryo-EM structure of  -galactosidase in complex with a cell-permeant inhibitor

(2015) A. Bartesaghi et al.   SCIENCE

Structural and evolutionary versatility in protein complexes with uneven stoichiometry

(2015) Joseph A. Marsh et al.   Nature Communications

Use B-factor related features for accurate classification between protein binding interfaces and crystal packing contacts

(2014) Qian Liu et al.   BMC BIOINFORMATICS

SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information

(2014) Marco Biasini et al.   NUCLEIC ACIDS RESEARCH

Differential Stability of the Crystallographic Interfaces of Mu- and Kappa-Opioid Receptors

(2014) Jennifer M. Johnston et al.   PLoS One

Protein-Protein Interface Detection Using the Energy Centrality Relationship (ECR) Characteristic of Proteins

(2014) Sanjana Sudarshan et al.   PLoS One

Single-residue insertion switches the quaternary structure and exciton states of cryptophyte light-harvesting proteins

(2014) Stephen J. Harrop et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effective discrimination between biologically relevant contacts and crystal packing contacts using new determinants

(2014) Jiesi Luo et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2014) Kumaran Baskaran et al.   BMC STRUCTURAL BIOLOGY

Quantitative analysis of mammalian GIRK2 channel regulation by G proteins, the signaling lipid PIP2 and Na+ in a reconstituted system

(2014) Weiwei Wang et al.   eLife

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

(2014) Sergey Ovchinnikov et al.   eLife

Structural Determinants of Oligomerization of Δ1-Pyrroline-5-Carboxylate Dehydrogenase: Identification of a Hexamerization Hot Spot

(2013) Min Luo et al.   JOURNAL OF MOLECULAR BIOLOGY

DockRank: Ranking docked conformations using partner-specific sequence homology-based protein interface prediction

(2013) Li C. Xue et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models

(2012) Iain H. Moal et al.   BIOINFORMATICS

Protein docking prediction using predicted protein-protein interface

(2012) Bin Li et al.   BMC BIOINFORMATICS

Protein interface classification by evolutionary analysis

(2012) Jose M Duarte et al.   BMC BIOINFORMATICS

How many packing contacts are observed in protein crystals?

(2012) Oliviero Carugo et al.   JOURNAL OF STRUCTURAL BIOLOGY

Macromolecular complexes in crystals and solutions

(2011) Evgeny Krissinel   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Overview of theCCP4 suite and current developments

(2011) Martyn D. Winn et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Combining Bayes Classification and Point Group Symmetry under Boolean Framework for Enhanced Protein Quaternary Structure Inference

(2011) Pralay Mitra et al.   STRUCTURE

The Subunit Interfaces of Weakly Associated Homodimeric Proteins

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

A Simple Definition of Structural Regions in Proteins and Its Use in Analyzing Interface Evolution

(2010) Emmanuel D. Levy   JOURNAL OF MOLECULAR BIOLOGY

The protein common interface database (ProtCID)--a comprehensive database of interactions of homologous proteins in multiple crystal forms

(2010) Q. Xu et al.   NUCLEIC ACIDS RESEARCH

The RCSB Protein Data Bank: redesigned web site and web services

(2010) P. W. Rose et al.   NUCLEIC ACIDS RESEARCH

PDBWiki: added value through community annotation of the Protein Data Bank

(2010) H. Stehr et al.   Database-The Journal of Biological Databases and Curation

Crystal contacts as nature's docking solutions

(2009) Evgeny Krissinel   JOURNAL OF COMPUTATIONAL CHEMISTRY

A Common Structural Basis for pH- and Calmodulin-mediated Regulation in Plant Glutamate Decarboxylase

(2009) Heinz Gut et al.   JOURNAL OF MOLECULAR BIOLOGY

Inferred Biomolecular Interaction Server—a web server to analyze and predict protein interacting partners and binding sites

(2009) Benjamin A. Shoemaker et al.   NUCLEIC ACIDS RESEARCH

Protein-protein crystal-packing contacts

(2009) Oliviero Carugo et al.   PROTEIN SCIENCE

Evolutionary conservation in multiple faces of protein interaction

(2009) Yoon Sup Choi et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Crystallography and protein–protein interactions: biological interfaces and crystal contacts

(2008) Bostjan Kobe et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

DiMoVo: a Voronoi tessellation-based method for discriminating crystallographic and biological protein-protein interactions

(2008) J. Bernauer et al.   BIOINFORMATICS

Biochemical and Structural Studies of Yeast Vps4 Oligomerization

(2008) Malgorzata D. Gonciarz et al.   JOURNAL OF MOLECULAR BIOLOGY

Statistical Analysis of Interface Similarity in Crystals of Homologous Proteins

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

Assembly reflects evolution of protein complexes

(2008) Emmanuel D. Levy et al.   NATURE

An unusually small dimer interface is observed in all available crystal structures of cytosolic sulfotransferases

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

Electrostatic contributions to protein-protein interactions: Fast energetic filters for docking and their physical basis

(2002) Raquel Norel et al.   PROTEIN SCIENCE