Statistical mechanics-based method to extract atomic distance-dependent potentials from protein structures

Inclusion of Solvation and Entropy in the Knowledge-Based Scoring Function for Protein−Ligand Interactions

(2010) Sheng-You Huang et al.   Journal of Chemical Information and Modeling

I-TASSER: a unified platform for automated protein structure and function prediction

(2010) Ambrish Roy et al.   Nature Protocols

Artefacts and biases affecting the evaluation of scoring functions on decoy sets for protein structure prediction

(2009) Julia Handl et al.   BIOINFORMATICS

Protein Structure Prediction by Pro-Sp3-TASSER

(2009) Hongyi Zhou et al.   BIOPHYSICAL JOURNAL

Generalized ensemble methods for de novo structure prediction

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

Progress and challenges in protein structure prediction

(2008) Yang Zhang   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functions

(2008) Yuedong Yang et al.   PROTEIN SCIENCE

An iterative knowledge-based scoring function for protein-protein recognition

(2008) Sheng-You Huang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Specific interactions for ab initio folding of protein terminal regions with secondary structures

(2008) Yuedong Yang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

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

OPUS-PSP: An Orientation-dependent Statistical All-atom Potential Derived from Side-chain Packing

(2007) Mingyang Lu et al.   JOURNAL OF MOLECULAR BIOLOGY

QMEAN: A comprehensive scoring function for model quality assessment

(2007) Pascal Benkert et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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