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Physics-Based Protein-Structure Prediction Using a Hierarchical Protocol Based on the UNRES Force Field: Assessment in Two Blind Tests

Proceedings of the National Academy of Sciences - PNAS, 2005-05, Vol.102 (21), p.7547-7552

2005

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Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field

The Journal of chemical physics, 2001-08, Vol.115 (5), p.2323-2347

2001

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Comparative genomic mapping of uncharacterized canine retinal ESTs to identify novel candidate genes for hereditary retinal disorders

Molecular vision, 2009-05, Vol.15, p.927-936

2009

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The protein folding problem: global optimization of the force fields

Frontiers in bioscience, 2004-09, Vol.9, p.3296

2004

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Clp Protease Complexes from Photosynthetic and Non-photosynthetic Plastids and Mitochondria of Plants, Their Predicted Three-dimensional Structures, and Functional Implications

The Journal of biological chemistry, 2004-02, Vol.279 (6), p.4768-4781

2004

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Enriching the sequence substitution matrix by structural information

Proteins, structure, function, and bioinformatics, 2004-01, Vol.54 (1), p.41-48

2004

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Recent Improvements in Prediction of Protein Structure by Global Optimization of a Potential Energy Function

Proceedings of the National Academy of Sciences - PNAS, 2001-02, Vol.98 (5), p.2329-2333

2001

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A Method for Optimizing Potential-Energy Functions by a Hierarchical Design of the Potential-Energy Landscape: Application to the UNRES Force Field

Proceedings of the National Academy of Sciences - PNAS, 2002-02, Vol.99 (4), p.1937-1942

2002

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P43-S Computational Biology Applications Suite for High-Performance Computing (BioHPC.net)

Journal of biomolecular techniques, 2007-02, Vol.18 (1), p.16-16

Pillardy, J.

2007

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Radiation hybrid map, physical map, and low-pass genomic sequence of the canine prcd region on CFA9 and comparative mapping with the syntenic region on human chromosome 17

Genomics (San Diego, Calif.), 2003-02, Vol.81 (2), p.138-148

2003

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Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 2. Off-Lattice Tests of the Method with Single Proteins

The journal of physical chemistry. B, 2004-10, Vol.108 (43), p.16934-16949

2004

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Protein Structure Prediction by Global Optimization of a Potential Energy Function

Proceedings of the National Academy of Sciences - PNAS, 1999-05, Vol.96 (10), p.5482-5485

1999

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Support vector training of protein alignment models

Journal of computational biology, 2008-09, Vol.15 (7), p.867

2008

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Packing Helices in Proteins by Global Optimization of a Potential Energy Function

Proceedings of the National Academy of Sciences - PNAS, 2003-02, Vol.100 (4), p.1706-1710

2003

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Optimization of Parameters in Macromolecular Potential Energy Functions by Conformational Space Annealing

The journal of physical chemistry. B, 2001-08, Vol.105 (30), p.7291-7298

2001

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BioHPC: Computational Biology Application Suite for High Performance Computing

Journal of biomolecular techniques, 2010-09, Vol.21 (3 Suppl), p.S23-S23

2010

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Improved conformational space annealing method to treat β-structure with the UNRES force-field and to enhance scalability of parallel implementation

Polymer (Guilford), 2004-01, Vol.45 (2), p.677-686

2004

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Conformation-Family Monte Carlo: A New Method for Crystal Structure Prediction

Proceedings of the National Academy of Sciences - PNAS, 2001-10, Vol.98 (22), p.12351-12356

2001

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An Efficient Deformation-Based Global Optimization Method (Self-Consistent Basin-to-Deformed-Basin Mapping (SCBDBM)). Application to Lennard-Jones Atomic Clusters

The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, 1999-11, Vol.103 (46), p.9370-9377

1999

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Development of Physics-Based Energy Functions that Predict Medium-Resolution Structures for Proteins of the α, β, and α/β Structural Classes

The journal of physical chemistry. B, 2001-08, Vol.105 (30), p.7299-7311

2001

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Calculation of protein conformation by global optimization of a potential energy function

Proteins, structure, function, and bioinformatics, 1999, Vol.37 (S3), p.204-208

1999

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Derivation of a New Force Field for Crystal-Structure Prediction Using Global Optimization: Nonbonded Potential Parameters for Hydrocarbons and Alcohols

The journal of physical chemistry. B, 2003-07, Vol.107 (29), p.7143-7154

2003

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Integrated Core Facility Support and Optimization of Next Generation Sequencing Technologies

Journal of biomolecular techniques, 2011-10, Vol.22 (Suppl), p.S32-S32

2011

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Computational Biology Service Unit: Cornell University Core Facility for Computational Biology

Journal of biomolecular techniques, 2010-09, Vol.21 (3 Suppl), p.S68-S68

2010

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Efficient parallel algorithms in global optimization of potential energy functions for peptides, proteins, and crystals

Computer physics communications, 2000-06, Vol.128 (1-2), p.399-411

2000

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Physics-Based Protein-Structure Prediction Using a Hierarchical Protocol Based on the UNRES Force Field: Assessment in Two Blind Tests

Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field

Comparative genomic mapping of uncharacterized canine retinal ESTs to identify novel candidate genes for hereditary retinal disorders

The protein folding problem: global optimization of the force fields

Clp Protease Complexes from Photosynthetic and Non-photosynthetic Plastids and Mitochondria of Plants, Their Predicted Three-dimensional Structures, and Functional Implications

Enriching the sequence substitution matrix by structural information

Recent Improvements in Prediction of Protein Structure by Global Optimization of a Potential Energy Function

A Method for Optimizing Potential-Energy Functions by a Hierarchical Design of the Potential-Energy Landscape: Application to the UNRES Force Field

P43-S Computational Biology Applications Suite for High-Performance Computing (BioHPC.net)

Radiation hybrid map, physical map, and low-pass genomic sequence of the canine prcd region on CFA9 and comparative mapping with the syntenic region on human chromosome 17

Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 2. Off-Lattice Tests of the Method with Single Proteins

Protein Structure Prediction by Global Optimization of a Potential Energy Function

Support vector training of protein alignment models

Packing Helices in Proteins by Global Optimization of a Potential Energy Function

Optimization of Parameters in Macromolecular Potential Energy Functions by Conformational Space Annealing

BioHPC: Computational Biology Application Suite for High Performance Computing

Improved conformational space annealing method to treat β-structure with the UNRES force-field and to enhance scalability of parallel implementation

Conformation-Family Monte Carlo: A New Method for Crystal Structure Prediction

An Efficient Deformation-Based Global Optimization Method (Self-Consistent Basin-to-Deformed-Basin Mapping (SCBDBM)). Application to Lennard-Jones Atomic Clusters

Development of Physics-Based Energy Functions that Predict Medium-Resolution Structures for Proteins of the α, β, and α/β Structural Classes

Calculation of protein conformation by global optimization of a potential energy function

Derivation of a New Force Field for Crystal-Structure Prediction Using Global Optimization: Nonbonded Potential Parameters for Hydrocarbons and Alcohols

Integrated Core Facility Support and Optimization of Next Generation Sequencing Technologies

Computational Biology Service Unit: Cornell University Core Facility for Computational Biology

Efficient parallel algorithms in global optimization of potential energy functions for peptides, proteins, and crystals

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