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DOCK 6: Impact of new features and current docking performance

Journal of computational chemistry, 2015-06, Vol.36 (15), p.1132-1156

2015

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DOCK 6: combining techniques to model RNA-small molecule complexes

RNA (Cambridge), 2009-06, Vol.15 (6), p.1219-1230

2009

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Apolipoprotein (Apo) E4 Enhances Amyloid β Peptide Production in Cultured Neuronal Cells: Apoe Structure as a Potential Therapeutic Target

Proceedings of the National Academy of Sciences - PNAS, 2005-12, Vol.102 (51), p.18700-18705

2005

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DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases

Journal of computer-aided molecular design, 2001-05, Vol.15 (5), p.411-428

2001

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Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions

Journal of chemical theory and computation, 2006-01, Vol.2 (1), p.128-139

2006

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Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods

Biopolymers, 2003-01, Vol.68 (1), p.16-34

2003

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Structure-Based Strategies for Drug Design and Discovery

Science (American Association for the Advancement of Science), 1992-08, Vol.257 (5073), p.1078-1082

Kuntz, Irwin D.

1992

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Hierarchical Database Screenings for HIV-1 Reverse Transcriptase Using a Pharmacophore Model, Rigid Docking, Solvation Docking, and MM−PB/SA

Journal of medicinal chemistry, 2005-04, Vol.48 (7), p.2432-2444

2005

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Development and validation of a modular, extensible docking program: DOCK 5

Journal of computer-aided molecular design, 2006-10, Vol.20 (10-11), p.601-619

2006

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Potent, Low-Molecular-Weight Non-Peptide Inhibitors of Malarial Aspartyl Protease Plasmepsin II

Journal of medicinal chemistry, 1999-04, Vol.42 (8), p.1428-1440

1999

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Inhibitors of Kinesin Activity from Structure-Based Computer Screening

Biochemistry (Easton), 2000-03, Vol.39 (10), p.2805-2814

2000

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Photochemically Knocking Out Glutamate Receptors in Vivo

Journal of the American Chemical Society, 2004-11, Vol.126 (43), p.13886-13887

2004

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Darwinian Docking

Journal of computer-aided molecular design, 2012, Vol.26 (1), p.73-75

Kuntz, Irwin D.

2012

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Structure-Based Discovery of Inhibitors of Thymidylate Synthase

Science (American Association for the Advancement of Science), 1993-03, Vol.259 (5100), p.1445-1450

1993

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Structure-Based Discovery of Ligands Targeted to the RNA Double Helix

Biochemistry (Easton), 1997-09, Vol.36 (38), p.11402-11407

1997

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Critical evaluation of search algorithms for automated molecular docking and database screening

Journal of computational chemistry, 1997-07, Vol.18 (9), p.1175-1189

1997

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High throughput Protein Fold Identification by Using Experimental Constraints Derived from Intramolecular Cross-Links and Mass Spectrometry

Proceedings of the National Academy of Sciences - PNAS, 2000-05, Vol.97 (11), p.5802-5806

2000

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Inclusion of Solvation in Ligand Binding Free Energy Calculations Using the Generalized-Born Model

Journal of the American Chemical Society, 1999-09, Vol.121 (35), p.8033-8043

1999

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Molecular Dynamics and Free Energy Analyses of Cathepsin D−Inhibitor Interactions: Insight into Structure-Based Ligand Design

Journal of medicinal chemistry, 2002-03, Vol.45 (7), p.1412-1419

2002

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Investigation of Neuraminidase-Substrate Recognition Using Molecular Dynamics and Free Energy Calculations

Journal of medicinal chemistry, 2003-12, Vol.46 (26), p.5628-5637

2003

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MOLECULAR RECOGNITION AND DOCKING ALGORITHMS

Annual review of biophysics and biomolecular structure, 2003-01, Vol.32 (1), p.335-373

2003

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Virtual Screening of Combinatorial Libraries across a Gene Family: in Search of Inhibitors of Giardia lamblia Guanine Phosphoribosyltransferase

Antimicrobial Agents and Chemotherapy, 2001-09, Vol.45 (9), p.2571-2576

2001

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A Molecular Basis for the Selectivity of Thiadiazole Urea Inhibitors with Stromelysin-1 and Gelatinase-A from Generalized Born Molecular Dynamics Simulations

Journal of medicinal chemistry, 2004-06, Vol.47 (12), p.3065-3074

2004

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Inhibition of Mycobacterium tuberculosis AhpD, an Element of the Peroxiredoxin Defense against Oxidative Stress

Antimicrobial Agents and Chemotherapy, 2004-07, Vol.48 (7), p.2424-2430

2004

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Partial Acetylation of Lysine Residues Improves Intraprotein Cross-Linking

Analytical chemistry (Washington), 2008-02, Vol.80 (4), p.951-960

2008

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DOCK 6: Impact of new features and current docking performance

DOCK 6: combining techniques to model RNA-small molecule complexes

Apolipoprotein (Apo) E4 Enhances Amyloid β Peptide Production in Cultured Neuronal Cells: Apoe Structure as a Potential Therapeutic Target

DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases

Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions

Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods

Structure-Based Strategies for Drug Design and Discovery

Hierarchical Database Screenings for HIV-1 Reverse Transcriptase Using a Pharmacophore Model, Rigid Docking, Solvation Docking, and MM−PB/SA

Development and validation of a modular, extensible docking program: DOCK 5

Potent, Low-Molecular-Weight Non-Peptide Inhibitors of Malarial Aspartyl Protease Plasmepsin II

Inhibitors of Kinesin Activity from Structure-Based Computer Screening

Photochemically Knocking Out Glutamate Receptors in Vivo

Darwinian Docking

Structure-Based Discovery of Inhibitors of Thymidylate Synthase

Structure-Based Discovery of Ligands Targeted to the RNA Double Helix

Critical evaluation of search algorithms for automated molecular docking and database screening

High throughput Protein Fold Identification by Using Experimental Constraints Derived from Intramolecular Cross-Links and Mass Spectrometry

Inclusion of Solvation in Ligand Binding Free Energy Calculations Using the Generalized-Born Model

Molecular Dynamics and Free Energy Analyses of Cathepsin D−Inhibitor Interactions: Insight into Structure-Based Ligand Design

Investigation of Neuraminidase-Substrate Recognition Using Molecular Dynamics and Free Energy Calculations

MOLECULAR RECOGNITION AND DOCKING ALGORITHMS

Virtual Screening of Combinatorial Libraries across a Gene Family: in Search of Inhibitors of Giardia lamblia Guanine Phosphoribosyltransferase

A Molecular Basis for the Selectivity of Thiadiazole Urea Inhibitors with Stromelysin-1 and Gelatinase-A from Generalized Born Molecular Dynamics Simulations

Inhibition of Mycobacterium tuberculosis AhpD, an Element of the Peroxiredoxin Defense against Oxidative Stress

Partial Acetylation of Lysine Residues Improves Intraprotein Cross-Linking

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