Optimized distance-dependent atom-pair-based potential DOOP for protein structure prediction

What is the best reference state for designing statistical atomic potentials in protein structure prediction?

(2013) Haiyou Deng et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Protein-Folding Problem, 50 Years On

(2012) K. A. Dill et al.   SCIENCE

A simple and efficient statistical potential for scoring ensembles of protein structures

(2012) Pilar Cossio et al.   Scientific Reports

GOAP: A Generalized Orientation-Dependent, All-Atom Statistical Potential for Protein Structure Prediction

(2011) Hongyi Zhou et al.   BIOPHYSICAL JOURNAL

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

(2010) Dmitry Rykunov et al.   BMC BIOINFORMATICS

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

(2010) Jian Zhang et al.   PLoS One

CHARMM: The biomolecular simulation program

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

Predicting protein complex geometries with a neural network

(2009) Myong-Ho Chae et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Progress and challenges in protein structure prediction

(2008) Yang Zhang   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

(2008) Yuedong Yang 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