Fast de novo discovery of low-energy protein loop conformations

Conformational sampling and structure prediction of multiple interacting loops in soluble andβ-barrel membrane proteins using multi-loop distance-guided chain-growth Monte Carlo method

(2015) Ke Tang et al.   BIOINFORMATICS

Fast Protein Loop Sampling and Structure Prediction Using Distance-Guided Sequential Chain-Growth Monte Carlo Method

(2014) Ke Tang et al.   PLoS Computational Biology

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

(2013) Shide Liang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Small-molecule ligand docking into comparative models with Rosetta

(2013) Steven A Combs et al.   Nature Protocols

Atomic-Accuracy Prediction of Protein Loop Structures through an RNA-Inspired Ansatz

(2013) Rhiju Das   PLoS One

Protein Loop Modeling with Optimized Backbone Potential Functions

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

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

The FALC-Loop web server for protein loop modeling

(2011) J. Ko et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Shide Liang 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

A Smoothed Backbone-Dependent Rotamer Library for Proteins Derived from Adaptive Kernel Density Estimates and Regressions

(2011) Maxim V. Shapovalov et al.   STRUCTURE

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

(2010) Ambrish Roy et al.   Nature Protocols

Protein loop modeling by using fragment assembly and analytical loop closure

(2010) Julian Lee et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling

(2009) Daniel J Mandell et al.   NATURE METHODS

A Self-Organizing Algorithm for Modeling Protein Loops

(2009) Pu Liu et al.   PLoS Computational Biology

DARS (Decoys As the Reference State) Potentials for Protein-Protein Docking

(2008) Gwo-Yu Chuang et al.   BIOPHYSICAL JOURNAL

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

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

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