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Cross-over between discrete and continuous protein structure space: insights into automatic classification and networks of protein structures

PLoS computational biology, 2009-03, Vol.5 (3), p.e1000331-e1000331

2009

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A new implicit solvent model for protein-ligand docking

Proteins, structure, function, and bioinformatics, 2007-05, Vol.67 (3), p.606-616

2007

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VSDMIP: virtual screening data management on an integrated platform

Journal of computer-aided molecular design, 2009-03, Vol.23 (3), p.171-184

2009

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Discovery of genomic alterations through coregulation analysis of closely linked genes: a frequent gain in 17q25.3 in prostate cancer

Annals of the New York Academy of Sciences, 2010-10, Vol.1210 (1), p.17-24

2010

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Co-regulation analysis of closely linked genes identifies a highly recurrent gain on chromosome 17q25.3 in prostate cancer

BMC cancer, 2008-10, Vol.8 (1), p.315-315, Article 315

2008

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Receptor-Based Virtual Screening and Biological Characterization of Human Apurinic/Apyrimidinic Endonuclease (Ape1) Inhibitors

ChemMedChem, 2012-12, Vol.7 (12), p.2168-2178

2012

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MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison

Protein science, 2002-11, Vol.11 (11), p.2606-2621

2002

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Structure-Based Discovery of Novel Non-nucleosidic DNA Alkyltransferase Inhibitors: Virtual Screening and in Vitro and in Vivo Activities

Journal of Chemical Information and Modeling, 2008-04, Vol.48 (4), p.844-854

2008

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Protein-protein interaction antagonists as novel inhibitors of non-canonical polyubiquitylation

PloS one, 2010-06, Vol.5 (6), p.e11403-e11403

2010

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Molecular basis of the differential interaction with lithium of glycine transporters GLYT1 and GLYT2

Journal of neurochemistry, 2011-07, Vol.118 (2), p.195-204

2011

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An Analysis of Core Deformations in Protein Superfamilies

Biophysical journal, 2005-02, Vol.88 (2), p.1291-1299

2005

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An aspartate residue in the external vestibule of GLYT2 (glycine transporter 2) controls cation access and transport coupling

Biochemical journal, 2012-03, Vol.442 (2), p.323-334

2012

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Improvement of Comparative Model Accuracy by Free-Energy Optimization along Principal Components of Natural Structural Variation

Proceedings of the National Academy of Sciences - PNAS, 2004-10, Vol.101 (43), p.15346-15351

2004

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CAFASP3: The third critical assessment of fully automated structure prediction methods

Proteins, structure, function, and bioinformatics, 2003, Vol.53 (S6), p.503-516

2003

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Comparative Binding Energy Analysis Considering Multiple Receptors: A Step toward 3D-QSAR Models for Multiple Targets

Journal of medicinal chemistry, 2006-10, Vol.49 (21), p.6241-6253

2006

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Comparative analysis of chloroplast genomes: functional annotation, genome-based phylogeny, and deduced evolutionary patterns

Genome research, 2002-04, Vol.12 (4), p.567-583

2002

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Prediction of Drug Binding Affinities by Comparative Binding Energy Analysis

Journal of medicinal chemistry, 1995-07, Vol.38 (14), p.2681-2691

1995

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Comparative Binding Energy Analysis of HIV-1 Protease Inhibitors: Incorporation of Solvent Effects and Validation as a Powerful Tool in Receptor-Based Drug Design

Journal of medicinal chemistry, 1998-03, Vol.41 (6), p.836-852

1998

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A new progressive-iterative algorithm for multiple structure alignment

Bioinformatics, 2005-08, Vol.21 (15), p.3255-3263

2005

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Solution structure of the hypothetical protein TA0095 from Thermoplasma acidophilum: A novel superfamily with a two‐layer sandwich architecture

Protein science, 2007-10, Vol.16 (10), p.2278-2286

2007

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Nativelike Topology Assembly of Small Proteins Using Predicted Restraints in Monte Carlo Folding Simulations

Proceedings of the National Academy of Sciences - PNAS, 1998-02, Vol.95 (3), p.1020-1025

1998

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Gene Discovery in Bladder Cancer Progression using cDNA Microarrays

The American journal of pathology, 2003-08, Vol.163 (2), p.505-516

2003

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Dual activation of pathways regulated by steroid receptors and peptide growth factors in primary prostate cancer revealed by Factor Analysis of microarray data

BMC genomics, 2005-08, Vol.6 (1), p.109-109, Article 109

2005

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Virtual Screening with Flexible Docking and COMBINE-Based Models. Application to a Series of Factor Xa Inhibitors

Journal of medicinal chemistry, 2004-02, Vol.47 (4), p.805-820

2004

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Effective connectivity profile: A structural representation that evidences the relationship between protein structures and sequences

Proteins, structure, function, and bioinformatics, 2008-12, Vol.73 (4), p.872-888

2008

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Cross-over between discrete and continuous protein structure space: insights into automatic classification and networks of protein structures

A new implicit solvent model for protein-ligand docking

VSDMIP: virtual screening data management on an integrated platform

Discovery of genomic alterations through coregulation analysis of closely linked genes: a frequent gain in 17q25.3 in prostate cancer

Co-regulation analysis of closely linked genes identifies a highly recurrent gain on chromosome 17q25.3 in prostate cancer

Receptor-Based Virtual Screening and Biological Characterization of Human Apurinic/Apyrimidinic Endonuclease (Ape1) Inhibitors

MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison

Structure-Based Discovery of Novel Non-nucleosidic DNA Alkyltransferase Inhibitors: Virtual Screening and in Vitro and in Vivo Activities

Protein-protein interaction antagonists as novel inhibitors of non-canonical polyubiquitylation

Molecular basis of the differential interaction with lithium of glycine transporters GLYT1 and GLYT2

An Analysis of Core Deformations in Protein Superfamilies

An aspartate residue in the external vestibule of GLYT2 (glycine transporter 2) controls cation access and transport coupling

Improvement of Comparative Model Accuracy by Free-Energy Optimization along Principal Components of Natural Structural Variation

CAFASP3: The third critical assessment of fully automated structure prediction methods

Comparative Binding Energy Analysis Considering Multiple Receptors: A Step toward 3D-QSAR Models for Multiple Targets

Comparative analysis of chloroplast genomes: functional annotation, genome-based phylogeny, and deduced evolutionary patterns

Prediction of Drug Binding Affinities by Comparative Binding Energy Analysis

Comparative Binding Energy Analysis of HIV-1 Protease Inhibitors: Incorporation of Solvent Effects and Validation as a Powerful Tool in Receptor-Based Drug Design

A new progressive-iterative algorithm for multiple structure alignment

Solution structure of the hypothetical protein TA0095 from Thermoplasma acidophilum: A novel superfamily with a two‐layer sandwich architecture

Nativelike Topology Assembly of Small Proteins Using Predicted Restraints in Monte Carlo Folding Simulations

Gene Discovery in Bladder Cancer Progression using cDNA Microarrays

Dual activation of pathways regulated by steroid receptors and peptide growth factors in primary prostate cancer revealed by Factor Analysis of microarray data

Virtual Screening with Flexible Docking and COMBINE-Based Models. Application to a Series of Factor Xa Inhibitors

Effective connectivity profile: A structural representation that evidences the relationship between protein structures and sequences

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