Integrating protein structural dynamics and evolutionary analysis with Bio3D

Domain-Opening and Dynamic Coupling in the α-Subunit of Heterotrimeric G Proteins

(2013) Xin-Qiu Yao et al.   BIOPHYSICAL JOURNAL

Evaluation of Protein Elastic Network Models Based on an Analysis of Collective Motions

(2013) Edvin Fuglebakk et al.   Journal of Chemical Theory and Computation

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Divergent evolution of protein conformational dynamics in dihydrofolate reductase

(2013) Gira Bhabha et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Effective Harmonic Potentials: Insights into the Internal Cooperativity and Sequence-Specificity of Protein Dynamics

(2013) Yves Dehouck et al.   PLoS Computational Biology

Measuring and comparing structural fluctuation patterns in large protein datasets

(2012) Edvin Fuglebakk et al.   BIOINFORMATICS

Determining Geometrically Stable Domains in Molecular Conformation Sets

(2012) Julia Romanowska et al.   Journal of Chemical Theory and Computation

NMSim Web Server: integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins

(2012) D. M. Kruger et al.   NUCLEIC ACIDS RESEARCH

An overview of the Amber biomolecular simulation package

(2012) Romelia Salomon-Ferrer et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

ProDy: Protein Dynamics Inferred from Theory and Experiments

(2011) A. Bakan et al.   BIOINFORMATICS

MAVENs: Motion analysis and visualization of elastic networks and structural ensembles

(2011) Michael T Zimmermann et al.   BMC BIOINFORMATICS

Crystal structure of the β2 adrenergic receptor–Gs protein complex

(2011) Søren G. F. Rasmussen et al.   NATURE

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Structural flexibility of the G s  -helical domain in the  2-adrenoceptor Gs complex

(2011) G. H. Westfield et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chaperonins: two rings for folding

(2011) Hugo Yébenes et al.   TRENDS IN BIOCHEMICAL SCIENCES

Validating and improving elastic network models with molecular dynamics simulations

(2010) Tod D. Romo et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Functional aspects of protein flexibility

(2009) Kaare Teilum et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Protein elastic network models and the ranges of cooperativity

(2009) L. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamical networks in tRNA:protein complexes

(2009) A. Sethi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sending Signals Dynamically

(2009) R. G. Smock et al.   SCIENCE

Discovery Through the Computational Microscope

(2009) Eric H. Lee et al.   STRUCTURE

Normal mode analysis for proteins

(2008) Lars Skjaerven et al.   JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM

Mapping the Nucleotide and Isoform-Dependent Structural and Dynamical Features of Ras Proteins

(2008) Alemayehu A. Gorfe et al.   STRUCTURE