CABS-flex: server for fast simulation of protein structure fluctuations

Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field

(2012) Michal Jamroz et al.   Journal of Chemical Theory and Computation

From Coarse-Grained to Atomic-Level Characterization of Protein Dynamics: Transition State for the Folding of B Domain of Protein A

(2012) Sebastian Kmiecik et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

Structural features that predict real-value fluctuations of globular proteins

(2012) Michal Jamroz et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Improving the Physical Realism and Structural Accuracy of Protein Models by a Two-Step Atomic-Level Energy Minimization

(2011) Dong Xu et al.   BIOPHYSICAL JOURNAL

A Normal Mode-Based Geometric Simulation Approach for Exploring Biologically Relevant Conformational Transitions in Proteins

(2011) Aqeel Ahmed et al.   Journal of Chemical Information and Modeling

Simulation of Chaperonin Effect on Protein Folding: A Shift from Nucleation–Condensation to Framework Mechanism

(2011) Sebastian Kmiecik et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

RosettaBackrub--a web server for flexible backbone protein structure modeling and design

(2010) F. Lauck et al.   NUCLEIC ACIDS RESEARCH

MoDEL (Molecular Dynamics Extended Library): A Database of Atomistic Molecular Dynamics Trajectories

(2010) Tim Meyer et al.   STRUCTURE

Modeling of loops in proteins: a multi-method approach

(2010) Michal Jamroz et al.   BMC STRUCTURAL BIOLOGY

Convergence and combination of methods in protein–protein docking

(2009) Sandor Vajda et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The role of dynamic conformational ensembles in biomolecular recognition

(2009) David D Boehr et al.   Nature Chemical Biology

Backrub-Like Backbone Simulation Recapitulates Natural Protein Conformational Variability and Improves Mutant Side-Chain Prediction

(2008) Colin A. Smith et al.   JOURNAL OF MOLECULAR BIOLOGY