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Computational methods in drug discovery

Beilstein journal of organic chemistry, 2016-12, Vol.12 (1), p.2694-2718

2016

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Iterative Molecular Dynamics–Rosetta Membrane Protein Structure Refinement Guided by Cryo-EM Densities

Journal of chemical theory and computation, 2017-10, Vol.13 (10), p.5131-5145

2017

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Using NMR Chemical Shifts and Cryo-EM Density Restraints in Iterative Rosetta-MD Protein Structure Refinement

Journal of chemical information and modeling, 2020-05, Vol.60 (5), p.2522-2532

2020

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Volumes and surface areas: geometries and scaling relationships between coarse- grained and atomic structures

Current pharmaceutical design, 2014, Vol.20 (8), p.1208-1222

2014

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Fold-specific sequence scoring improves protein sequence matching

BMC bioinformatics, 2016-08, Vol.17 (1), p.328-328, Article 328

2016

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The importance of slow motions for protein functional loops

Physical biology, 2012-02, Vol.9 (1), p.014001-014001

2012

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Predicting Protein Secondary Structure Using Consensus Data Mining (CDM) Based on Empirical Statistics and Evolutionary Information

Methods in molecular biology (Clifton, N.J.), 2017-01, Vol.1484, p.35

2017

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Predicting Designability of Small Proteins from Graph Features of Contact Maps

Journal of computational biology, 2016-05, Vol.23 (5), p.400-411

2016

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Multibody coarse-grained potentials for native structure recognition and quality assessment of protein models

Proteins, structure, function, and bioinformatics, 2011-06, Vol.79 (6), p.1923-1929

2011

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Combining Statistical Potentials with Dynamics-Based Entropies Improves Selection from Protein Decoys and Docking Poses

The journal of physical chemistry. B, 2012-06, Vol.116 (23), p.6725-6731

2012

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Exploration of the relationship between topology and designability of conformations

The Journal of chemical physics, 2011-06, Vol.134 (23), p.235101-235101-6

2011

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Multibody coarse-grained potentials for native structure recognition and quality assessment of protein models

Proteins, structure, function, and bioinformatics, 2014-07, Vol.82 (7), p.1549-1549

2014

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Diversity of Sequences Folding to Highly and Poorly Designable Structures

Biophysical journal, 2012-01, Vol.102 (3), p.456a-456a

2012

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Free energies for coarse-grained proteins by integrating multibody statistical contact potentials with entropies from elastic network models

Journal of structural and functional genomics, 2011-07, Vol.12 (2), p.137-147

2011

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Incorporating Protein Topology Information in Similarity Matrices for Improved Sequence Matching (A Fold-Specific Scoring System)

Biophysical journal, 2013-01, Vol.104 (2), p.508a-508a

2013

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Multi-Body Coarse-Grained Potentials for Native Structure Recognition and Quality Assessment of Protein Models

Proteins, structure, function, and bioinformatics, 2011-04, Vol.79 (6), p.1923-1929

2011

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IMPROVING PROTEIN STRUCTURE PREDICTION, REFINEMENT AND QUALITY ASSESSMENT TECHNIQUES

T.A.S.K. quarterly, 2014-07, Vol.18 (3)

2014

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Exploration of Designability of Proteins Using Graph Features of Contact Maps: Beyond Lattice Models

Research in Computational Molecular Biology, 2015, Vol.9029, p.188-201

2015

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Computational methods in drug discovery

Iterative Molecular Dynamics–Rosetta Membrane Protein Structure Refinement Guided by Cryo-EM Densities

Using NMR Chemical Shifts and Cryo-EM Density Restraints in Iterative Rosetta-MD Protein Structure Refinement

Volumes and surface areas: geometries and scaling relationships between coarse- grained and atomic structures

Fold-specific sequence scoring improves protein sequence matching

The importance of slow motions for protein functional loops

Predicting Protein Secondary Structure Using Consensus Data Mining (CDM) Based on Empirical Statistics and Evolutionary Information

Predicting Designability of Small Proteins from Graph Features of Contact Maps

Multibody coarse-grained potentials for native structure recognition and quality assessment of protein models

Combining Statistical Potentials with Dynamics-Based Entropies Improves Selection from Protein Decoys and Docking Poses

Exploration of the relationship between topology and designability of conformations

Multibody coarse-grained potentials for native structure recognition and quality assessment of protein models

Diversity of Sequences Folding to Highly and Poorly Designable Structures

Free energies for coarse-grained proteins by integrating multibody statistical contact potentials with entropies from elastic network models

Incorporating Protein Topology Information in Similarity Matrices for Improved Sequence Matching (A Fold-Specific Scoring System)

Multi-Body Coarse-Grained Potentials for Native Structure Recognition and Quality Assessment of Protein Models

IMPROVING PROTEIN STRUCTURE PREDICTION, REFINEMENT AND QUALITY ASSESSMENT TECHNIQUES

Exploration of Designability of Proteins Using Graph Features of Contact Maps: Beyond Lattice Models

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