Evolutionary Conserved Positions Define Protein Conformational Diversity

Conformational diversity and the emergence of sequence signatures during evolution

(2015) Gustavo Parisi et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

A Coarse-Grained Elastic Network Atom Contact Model and Its Use in the Simulation of Protein Dynamics and the Prediction of the Effect of Mutations

(2014) Vincent Frappier et al.   PLoS Computational Biology

CoDNaS: a database of conformational diversity in the native state of proteins

(2013) A. M. Monzon et al.   BIOINFORMATICS

Exploiting Conformational Ensembles in Modeling Protein–Protein Interactions on the Proteome Scale

(2013) Guray Kuzu et al.   JOURNAL OF PROTEOME RESEARCH

Protein Conformational Diversity Correlates with Evolutionary Rate

(2013) Diego Javier Zea et al.   MOLECULAR BIOLOGY AND EVOLUTION

BeEP Server: using evolutionary information for quality assessment of protein structure models

(2013) Nicolas Palopoli et al.   NUCLEIC ACIDS RESEARCH

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

Ensemble-based characterization of unbound and bound states on protein energy landscape

(2013) Anatoly M. Ruvinsky et al.   PROTEIN SCIENCE

Allostery and the Monod-Wyman-Changeux Model After 50 Years

(2012) Jean-Pierre Changeux   Annual Review of Biophysics

Protein dynamics and conformational selection in bidirectional signal transduction

(2012) Ruth Nussinov et al.   BMC BIOLOGY

Generation of Receptor Structural Ensembles for Virtual Screening Using Binding Site Shape Analysis and Clustering

(2012) David J. Osguthorpe et al.   Chemical Biology & Drug Design

Sequence Evolution Correlates with Structural Dynamics

(2012) Ying Liu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Protein Conformational Diversity Modulates Sequence Divergence

(2012) Ezequiel Juritz et al.   MOLECULAR BIOLOGY AND EVOLUTION

BioLiP: a semi-manually curated database for biologically relevant ligand–protein interactions

(2012) Jianyi Yang et al.   NUCLEIC ACIDS RESEARCH

RING: networking interacting residues, evolutionary information and energetics in protein structures

(2011) A. J. M. Martin et al.   BIOINFORMATICS

Identification of key residues for protein conformational transition using elastic network model

(2011)   JOURNAL OF CHEMICAL PHYSICS

An overview of in silico protein function prediction

(2010) Roy D. Sleator et al.   ARCHIVES OF MICROBIOLOGY

Automatic prediction of catalytic residues by modeling residue structural neighborhood

(2010) Elisa Cilia et al.   BMC BIOINFORMATICS

Protein dynamics and allostery: an NMR view

(2010) Shiou-Ru Tzeng et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Protein functional landscapes, dynamics, allostery: a tortuous path towards a universal theoretical framework

(2010) Pavel I. Zhuravlev et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Coupling between Normal Modes Drives Protein Conformational Dynamics: Illustrations Using Allosteric Transitions in Myosin II

(2009) Wenjun Zheng et al.   BIOPHYSICAL JOURNAL

From protein sequences to 3D-structures and beyond: the example of the UniProt Knowledgebase

(2009) Ursula Hinz et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Amplification and Detection of Single-Molecule Conformational Fluctuation through a Protein Interaction Network with Bimodal Distributions

(2009) Zhanghan Wu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Protein Dynamism and Evolvability

(2009) N. Tokuriki et al.   SCIENCE

Large-scale evaluation of dynamically important residues in proteins predicted by the perturbation analysis of a coarse-grained elastic model

(2009) Wenjun Zheng et al.   BMC STRUCTURAL BIOLOGY

Solution structure and catalytic mechanism of human protein histidine phosphatase 1

(2008) Weibin Gong et al.   BIOCHEMICAL JOURNAL

Exploring the Suitability of Coarse-Grained Techniques for the Representation of Protein Dynamics

(2008) Agustí Emperador et al.   BIOPHYSICAL JOURNAL

Restricted Mobility of Conserved Residues in Protein-Protein Interfaces in Molecular Simulations

(2008) Osman N. Yogurtcu et al.   BIOPHYSICAL JOURNAL

Exploring the structure and function paradigm

(2008) Oliver C. Redfern et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Evolutionary conservation of protein vibrational dynamics

(2008) Sandra Maguid et al.   GENE

Selected-fit versus induced-fit protein binding: Kinetic differences and mutational analysis

(2008) Thomas R. Weikl et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Iterative cluster-NMA: A tool for generating conformational transitions in proteins

(2008) Adam D. Schuyler et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution

(2008) O. F. Lange et al.   SCIENCE