Comparison between self-guided Langevin dynamics and molecular dynamics simulations for structure refinement of protein loop conformations

Toward canonical ensemble distribution from self-guided Langevin dynamics simulation

(2011) Xiongwu Wu et al.   JOURNAL OF CHEMICAL PHYSICS

Protein Folding Simulations Combining Self-Guided Langevin Dynamics and Temperature-Based Replica Exchange

(2010) Michael S. Lee et al.   Journal of Chemical Theory and Computation

Assessment of the protein-structure refinement category in CASP8

(2009) Justin L. MacCallum et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Structure prediction for CASP8 with all-atom refinement using Rosetta

(2009) Srivatsan Raman et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Development of a Physics-Based Force Field for the Scoring and Refinement of Protein Models

(2008) Liliana Wroblewska et al.   BIOPHYSICAL JOURNAL

Prediction of Protein Loop Conformations Using the AGBNP Implicit Solvent Model and Torsion Angle Sampling

(2008) Anthony K. Felts et al.   Journal of Chemical Theory and Computation

Calculation of Protein Heat Capacity from Replica-Exchange Molecular Dynamics Simulations with Different Implicit Solvent Models

(2008) In-Chul Yeh et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Protein model refinement using an optimized physics-based all-atom force field

(2008) A. Jagielska et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Solvent dramatically affects protein structure refinement

(2008) G. Chopra et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Refining homology models by combining replica-exchange molecular dynamics and statistical potentials

(2008) Jiang Zhu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Toward better refinement of comparative models: Predicting loops in inexact environments

(2008) Benjamin D. Sellers et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions

(2007) Mark A. Olson et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

(2002) Hongyi Zhou et al.   PROTEIN SCIENCE