Template based protein structure modeling by global optimization in CASP11

Sigma-RF: prediction of the variability of spatial restraints in template-based modeling by random forest

(2015) Juyong Lee et al.   BMC BIOINFORMATICS

lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests

(2013) Valerio Mariani et al.   BIOINFORMATICS

Hidden Information Revealed by Optimal Community Structure from a Protein-Complex Bipartite Network Improves Protein Function Prediction

(2013) Juyong Lee et al.   PLoS One

Protein structure modeling for CASP10 by multiple layers of global optimization

(2013) Keehyoung Joo et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assessment of template-based protein structure predictions in CASP10

(2013) Yuanpeng J. Huang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Modularity optimization by conformational space annealing

(2012) Juyong Lee et al.   PHYSICAL REVIEW E

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

(2011) Hongyi Zhou et al.   BIOPHYSICAL JOURNAL

De novo protein structure prediction by dynamic fragment assembly and conformational space annealing

(2011) Juyong Lee et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The other 90% of the protein: Assessment beyond the Cαs for CASP8 template-based and high-accuracy models

(2009) Daniel A. Keedy et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Improved prediction of protein side-chain conformations with SCWRL4

(2009) Georgii G. Krivov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8

(2009) Elmar Krieger et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Multiple Sequence Alignment by Conformational Space Annealing

(2008) Keehyoung Joo et al.   BIOPHYSICAL JOURNAL

All-atom chain-building by optimizing MODELLER energy function using conformational space annealing

(2008) Keehyoung Joo 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