A Novel Side-Chain Orientation Dependent Potential Derived from Random-Walk Reference State for Protein Fold Selection and Structure Prediction

New statistical potential for quality assessment of protein models and a survey of energy functions

(2010) Dmitry Rykunov et al.   BMC BIOINFORMATICS

Explicit Orientation Dependence in Empirical Potentials and Its Significance to Side-Chain Modeling

(2009) Jianpeng Ma   ACCOUNTS OF CHEMICAL RESEARCH

Protein structure prediction: when is it useful?

(2009) Yang Zhang   CURRENT OPINION IN STRUCTURAL BIOLOGY

CHARMM: The biomolecular simulation program

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

QMEAN server for protein model quality estimation

(2009) Pascal Benkert et al.   NUCLEIC ACIDS RESEARCH

Critical assessment of methods of protein structure prediction-Round VIII

(2009) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks

(2009) Yunqi Li et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

I-TASSER: Fully automated protein structure prediction in CASP8

(2009) Yang Zhang   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Splitting statistical potentials into meaningful scoring functions: Testing the prediction of near-native structures from decoy conformations

(2009) Patrick Aloy et al.   BMC STRUCTURAL BIOLOGY

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

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

A knowledge-based structure-discriminating function that requires only main-chain atom coordinates

(2008) Yoshihide Makino et al.   BMC STRUCTURAL BIOLOGY

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

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

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