Conformational diversity analysis reveals three functional mechanisms in proteins

DisProt 7.0: a major update of the database of disordered proteins

(2016) Damiano Piovesan et al.   NUCLEIC ACIDS RESEARCH

CoDNaS 2.0: a comprehensive database of protein conformational diversity in the native state

(2016) Alexander Miguel Monzon et al.   Database-The Journal of Biological Databases and Curation

Conformational diversity and the emergence of sequence signatures during evolution

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

Allostery without a conformational change? Revisiting the paradigm

(2015) Ruth Nussinov et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Insights on Structural Characteristics and Ligand Binding Mechanisms of CDK2

(2015) Yan Li et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Decoding the Mobility and Time Scales of Protein Loops

(2015) Yina Gu et al.   Journal of Chemical Theory and Computation

Anatomy of enzyme channels

(2014) Lukáš Pravda et al.   BMC BIOINFORMATICS

Classification of Intrinsically Disordered Regions and Proteins

(2014) Robin van der Lee et al.   CHEMICAL REVIEWS

MobiDB 2.0: an improved database of intrinsically disordered and mobile proteins

(2014) Emilio Potenza et al.   NUCLEIC ACIDS RESEARCH

MOLE 2.0: advanced approach for analysis of biomacromolecular channels

(2013) David Sehnal et al.   Journal of Cheminformatics

A Single Mutation in a Tunnel to the Active Site Changes the Mechanism and Kinetics of Product Release in Haloalkane Dehalogenase LinB

(2012) Lada Biedermannová et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels

(2012) K. Berka et al.   NUCLEIC ACIDS RESEARCH

Intrinsically disordered proteins: a 10-year recap

(2012) Peter Tompa   TRENDS IN BIOCHEMICAL SCIENCES

CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures

(2012) Eva Chovancova et al.   PLoS Computational Biology

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

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

Divergence and Convergence in Enzyme Evolution: Parallel Evolution of Paraoxonases from Quorum-quenching Lactonases

(2011) Mikael Elias et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Diversity of Function-Related Conformational Changes in Proteins: Coordinate Uncertainty, Fragment Rigidity, and Stability

(2010) Alexander A. Rashin et al.   BIOCHEMISTRY

3V: cavity, channel and cleft volume calculator and extractor

(2010) N. R. Voss et al.   NUCLEIC ACIDS RESEARCH

Enlarged representative set of protein structures

(2010) Uwe Hobohm et al.   PROTEIN SCIENCE

Convergent evolution of similar enzymatic function on different protein folds: The hexokinase, ribokinase, and galactokinase families of sugar kinases

(2010) Peer Bork et al.   PROTEIN SCIENCE

Fpocket: An open source platform for ligand pocket detection

(2009) Vincent Le Guilloux et al.   BMC BIOINFORMATICS

Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure

(2009) P. V. Burra et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein function annotation by homology-based inference

(2009) Yaniv Loewenstein et al.   GENOME BIOLOGY

Allostery: Absence of a Change in Shape Does Not Imply that Allostery Is Not at Play

(2008) Chung-Jung Tsai et al.   JOURNAL OF MOLECULAR BIOLOGY

Flexibility of Human Cytochromes P450: Molecular Dynamics Reveals Differences between CYPs 3A4, 2C9, and 2A6, which Correlate with Their Substrate Preferences

(2008) Josef Skopalík et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Allostery and cooperativity revisited

(2008) Qiang Cui et al.   PROTEIN SCIENCE