LEAP: Highly accurate prediction of protein loop conformations by integrating coarse-grained sampling and optimized energy scores with all-atom refinement of backbone and side chains

Prediction of Long Loops with Embedded Secondary Structure Using the Protein Local Optimization Program

(2013) Edward B. Miller et al.   Journal of Chemical Theory and Computation

Modeling Structures and Motions of Loops in Protein Molecules

(2012) Amarda Shehu et al.   Entropy

Protein Loop Modeling with Optimized Backbone Potential Functions

(2012) Shide Liang et al.   Journal of Chemical Theory and Computation

Structure Prediction of Loops with Fixed and Flexible Stems

(2012) A. Subramani et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Fast and accurate prediction of protein side-chain conformations

(2011) Shide Liang et al.   BIOINFORMATICS

Sampling Multiple Scoring Functions Can Improve Protein Loop Structure Prediction Accuracy

(2011) Yaohang Li et al.   Journal of Chemical Information and Modeling

Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions

(2011) Shide Liang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Characterizing the Existing and Potential Structural Space of Proteins by Large-Scale Multiple Loop Permutations

(2011) Liang Dai et al.   JOURNAL OF MOLECULAR BIOLOGY

Protein loop selection using orientation-dependent force fields derived by parameter optimization

(2011) Shide Liang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assessment of template based protein structure predictions in CASP9

(2011) Valerio Mariani et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Progress in super long loop prediction

(2011) Suwen Zhao et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The VSGB 2.0 model: A next generation energy model for high resolution protein structure modeling

(2011) Jianing Li et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Improving predicted protein loop structure ranking using a Pareto-optimality consensus method

(2010) Yaohang Li et al.   BMC STRUCTURAL BIOLOGY

LOOPER: a molecular mechanics-based algorithm for protein loop prediction

(2008) V. Z. Spassov et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Reconstruction of Protein Backbones from the BriX Collection of Canonical Protein Fragments

(2008) Lies Baeten et al.   PLoS Computational Biology

Side-chain modeling with an optimized scoring function

(2002) Shide Liang et al.   PROTEIN SCIENCE

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