Combining protein sequence, structure, and dynamics: A novel approach for functional evolution analysis of PAS domain superfamily

Signaling States of a Short Blue-Light Photoreceptor Protein PpSB1-LOV Revealed from Crystal Structures and Solution NMR Spectroscopy

(2016) Katrin Röllen et al.   JOURNAL OF MOLECULAR BIOLOGY

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Causes of evolutionary rate variation among protein sites

(2016) Julian Echave et al.   NATURE REVIEWS GENETICS

Comparing the intrinsic dynamics of multiple protein structures using elastic network models

(2015) Edvin Fuglebakk et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

A Gaussian network model study suggests that structural fluctuations are higher for inactive states than active states of protein kinases

(2015) Raju Kalaivani et al.   Molecular BioSystems

A Hinge Migration Mechanism Unlocks the Evolution of Green-to-Red Photoconversion in GFP-like Proteins

(2015) Hanseong Kim et al.   STRUCTURE

Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models

(2015) Hyuntae Na et al.   PLoS Computational Biology

Evolution of Conformational Dynamics Determines the Conversion of a Promiscuous Generalist into a Specialist Enzyme

(2014) T. Zou et al.   MOLECULAR BIOLOGY AND EVOLUTION

Computing protein dynamics from protein structure with elastic network models

(2014) Ugo Bastolla   Wiley Interdisciplinary Reviews-Computational Molecular Science

Structural dynamics flexibility informs function and evolution at a proteome scale

(2013) Zeynep Nevin Gerek et al.   Evolutionary Applications

The Amino-Terminal Helix Modulates Light-Activated Conformational Changes in AsLOV2

(2012) Josiah P. Zayner et al.   JOURNAL OF MOLECULAR BIOLOGY

Structural Basis for the Slow Dark Recovery of a Full-Length LOV Protein from Pseudomonas putida

(2012) Franco Circolone et al.   JOURNAL OF MOLECULAR BIOLOGY

Sequence Evolution Correlates with Structural Dynamics

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

Evolution of Three LOV Blue Light Receptor Families in Green Plants and Photosynthetic Stramenopiles: Phototropin, ZTL/FKF1/LKP2 and Aureochrome

(2012) Noriyuki Suetsugu et al.   PLANT AND CELL PHYSIOLOGY

STRUCTURE FLUCTUATIONS AND CONFORMATIONAL CHANGES IN PROTEIN BINDING

(2012) ANATOLY M. RUVINSKY et al.   Journal of Bioinformatics and Computational Biology

Ligand-Binding PAS Domains in a Genomic, Cellular, and Structural Context

(2010) Jonathan T. Henry et al.   Annual Review of Microbiology

REACH Coarse-Grained Normal Mode Analysis of Protein Dimer Interaction Dynamics

(2009) Kei Moritsugu et al.   BIOPHYSICAL JOURNAL

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Structure of PAS-Linked Histidine Kinase and the Response Regulator Complex

(2009) Seiji Yamada et al.   STRUCTURE

MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences

(2008) S. Kumar et al.   BRIEFINGS IN BIOINFORMATICS

Evolutionary conservation of protein vibrational dynamics

(2008) Sandra Maguid et al.   GENE