Princeton_TIGRESS: Protein geometry refinement using simulations and support vector machines

GalaxyRefine: protein structure refinement driven by side-chain repacking

(2013) Lim Heo et al.   NUCLEIC ACIDS RESEARCH

3Drefine: Consistent protein structure refinement by optimizing hydrogen bonding network and atomic-level energy minimization

(2013) Debswapna Bhattacharya et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Improved model quality assessment using ProQ2

(2012) Arjun Ray et al.   BMC BIOINFORMATICS

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

(2012) Andreas W. Götz et al.   Journal of Chemical Theory and Computation

Protein Structure Refinement through Structure Selection and Averaging from Molecular Dynamics Ensembles

(2012) Vahid Mirjalili et al.   Journal of Chemical Theory and Computation

Template-based protein structure modeling using the RaptorX web server

(2012) Morten Källberg et al.   Nature Protocols

KoBaMIN: a knowledge-based minimization web server for protein structure refinement

(2012) J. P. G. L. M. Rodrigues et al.   NUCLEIC ACIDS RESEARCH

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

LIBSVM

(2012) Chih-Chung Chang et al.   ACM Transactions on Intelligent Systems and Technology

ASTRO-FOLD 2.0: An enhanced framework for protein structure prediction

(2011) A. Subramani et al.   AICHE JOURNAL

APOLLO: a quality assessment service for single and multiple protein models

(2011) Z. Wang et al.   BIOINFORMATICS

Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates

(2011) Y. Yang et al.   BIOINFORMATICS

A machine learning-based method for protein global model quality assessment

(2011) Qiwen Dong et al.   INTERNATIONAL JOURNAL OF GENERAL SYSTEMS

Refinement of protein termini in template-based modeling using conformational space annealing

(2011) Hahnbeom Park et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assessment of protein structure refinement in CASP9

(2011) Justin L. MacCallum et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Atomic-Level Protein Structure Refinement Using Fragment-Guided Molecular Dynamics Conformation Sampling

(2011) Jian Zhang et al.   STRUCTURE

MULTICOM: a multi-level combination approach to protein structure prediction and its assessments in CASP8

(2010) Z. Wang et al.   BIOINFORMATICS

Sphericity of a protein via the -complex

(2010) Deok-Soo Kim et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Amyloid-like self-assembly of a dodecapeptide sequence from the adenovirus fiber shaft: Perspectives from molecular dynamics simulations

(2010) Phanourios Tamamis et al.   JOURNAL OF NON-CRYSTALLINE SOLIDS

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

(2010) Ambrish Roy et al.   Nature Protocols

CHARMM: The biomolecular simulation program

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

Amyloid-Like Self-Assembly of Peptide Sequences from the Adenovirus Fiber Shaft: Insights from Molecular Dynamics Simulations

(2009) Phanourios Tamamis et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Assessment of the protein-structure refinement category in CASP8

(2009) Justin L. MacCallum et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Development of a Physics-Based Force Field for the Scoring and Refinement of Protein Models

(2008) Liliana Wroblewska et al.   BIOPHYSICAL JOURNAL

Protein model refinement using an optimized physics-based all-atom force field

(2008) A. Jagielska et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Solvent dramatically affects protein structure refinement

(2008) G. Chopra et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2008) Yuedong Yang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Evaluating the absolute quality of a single protein model using structural features and support vector machines

(2008) Zheng Wang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

FACTS: Fast analytical continuum treatment of solvation

(2007) Urs Haberthür et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY