Automated generation of MCSS‐derived pharmacophoric DOCK site points for searching multiconformation databases

No abstract is available for this paper.

• Publication year

  2003

• Venue

  Proteins: Structure, Function, and Bioinformatics

• Publication date

  2003-05-01

• Fields of study

  Medicine, Chemistry, Computer Science

• Identifiers
  DOI 10.1002/prot.10296PMID 12660988
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Pharmacophore‐based molecular docking to account for ligand flexibility

  2003cited by this paper
• DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases

  2001cited by this paper
• Crystal structures of substrate binding to Bacillus subtilis holo-(acyl carrier protein) synthase reveal a novel trimeric arrangement of molecules resulting in three active sites.

  2000influential reference
• Recent advances in solid-phase chemical methodologies.

  1999cited by this paper
• Pro-1 of macrophage migration inhibitory factor functions as a catalytic base in the phenylpyruvate tautomerase activity.

  1999influential reference
• Ligand solvation in molecular docking

  1999cited by this paper
• Computational approaches to structure-based ligand design.

  1999cited by this paper
• Developments in solution-phase combinatorial chemistry.

  1999cited by this paper
• Protein structure prediction.

  1998cited by this paper
• All-atom empirical potential for molecular modeling and dynamics studies of proteins.

  1998cited by this paper
• Virtual screening : an overview

  1998cited by this paper
• Flexible ligand docking using conformational ensembles

  1998cited by this paper
• Marrying structure and genomics.

  1998cited by this paper
• Meeting review: the Second meeting on the Critical Assessment of Techniques for Protein Structure Prediction (CASP2), Asilomar, California, December 13-16, 1996.

  1997cited by this paper
• Theory of protein folding: the energy landscape perspective.

  1997cited by this paper
• The chemical-biological interface: developments in automated and miniaturised screening technology.

  1997cited by this paper
• Bioinformatics: from genome data to biological knowledge.

  1997cited by this paper
• An Experimental Approach to Mapping the Binding Surfaces of Crystalline Proteins

  1996cited by this paper
• Inhibition and catalytic mechanism of HIV-1 aspartic protease.

  1996cited by this paper
• Comparison of experimental and computational functional group mapping of an RNase A structure: implications for computer-aided drug design.

  1996cited by this paper
• Discovering High-Affinity Ligands for Proteins: SAR by NMR

  1996cited by this paper
• A second generation force field for the simulation of proteins

  1995cited by this paper
• On the use of LUDI to search the Fine Chemicals Directory for ligands of proteins of known three-dimensional structure

  1994cited by this paper
• Structure-based discovery of inhibitors of thymidylate synthase.

  1993cited by this paper
• LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads

  1992cited by this paper
• Automated docking with grid‐based energy evaluation

  1992cited by this paper
• Structure-Based Strategies for Drug Design and Discovery

  1992cited by this paper
• Functionality maps of binding sites: A multiple copy simultaneous search method

  1991cited by this paper
• A computational procedure for determining energetically favorable binding sites on biologically important macromolecules.

  1985cited by this paper
• CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

  1983cited by this paper
• A geometric approach to macromolecule-ligand interactions.

  1982cited by this paper
• Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A resolution. I. General features and binding of methotrexate.

  1982cited by this paper

• Structure-based pharmacophore modeling 2. Developing a novel framework for structure-based pharmacophore model generation and selection.

  2023cites this paper
• Structure-based pharmacophore modeling 1. Automated random pharmacophore model generation.

  2023cites this paper
• AutoPH4: An Automated Method for Generating Pharmacophore Models from Protein Binding Pockets

  2020cites this paper
• Quantum mechanics implementation in drug-design workflows: does it really help?

  2017cites this paper
• Computational solvent mapping in structure-based drug design.

  2015cites this paper
• Pharmacophore Modeling using Site-Identification by Ligand Competitive Saturation (SILCS) Method with Multiple Probe Molecules

  2015cites this paper
• Identification of anti-cancer agents using integrated computational tools.

  2015cites this paper
• Pharmacophore Modeling Using Site-Identification by Ligand Competitive Saturation (SILCS) with Multiple Probe Molecules

  2015cites this paper
• Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling

  2014cites this paper
• Pharmacophore-Based Similarity Scoring for DOCK

  2014influential citation
• Fragment-Based Lead Discovery and Design

  2014cites this paper
• Message passing interface and multithreading hybrid for parallel molecular docking of large databases on petascale high performance computing machines

  2013cites this paper
• IDENTIFICATION OF NOVEL INHIBITORS OF 11B- HYDROXYSTEROID DEHYDROGENASE TYPE 1FROM NATURAL PRODUCTS LIBRARY THROUGH DOCKING AND PHARMACOPHORE MODELING

  2012cites this paper
• Discovery of Novel 11β-HSD1 Inhibitors by Pharmacophore-Based Virtual Screening

  2012cites this paper
• Structure-Based Virtual Screening Using Index Technology

  2011cites this paper
• Pharmacophore based virtual screening, molecular docking studies to design potent heat shock protein 90 inhibitors.

  2011cites this paper
• Pharmacophore inference and its application to computational drug discovery

  2011cites this paper
• Identification and characterization of acidic mammalian chitinase inhibitors.

  2010cites this paper
• Recent Trends in Structure‐Based Drug Design and Energetics

  2010cites this paper
• Structure-based virtual screening for identification of novel 11 beta-HSD1 inhibitors

  2009cites this paper
• Structure-based virtual screening for identification of novel 11beta-HSD1 inhibitors.

  2009cites this paper
• Prospective ligand- and target-based 3D QSAR: state of the art 2008.

  2009cites this paper
• Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy

  2009cites this paper
• Challenges of fragment screening

  2009cites this paper
• The multi-copy simultaneous search methodology: a fundamental tool for structure-based drug design

  2009cites this paper
• In Silico Screening of Novel Inhibitors for HPV: A Rational Structure Based Approach (Docking Versus Pharmacophore Model Generation)

  2009cites this paper
• Investigation of MM-PBSA Rescoring of Docking Poses

  2008cites this paper
• Automated clustering of probe molecules from solvent mapping of protein surfaces: new algorithms applied to hot-spot mapping and structure-based drug design

  2008cites this paper
• Protein flexibility and species specificity in structure-based drug discovery: dihydrofolate reductase as a test system.

  2007cites this paper
• Exploring experimental sources of multiple protein conformations in structure-based drug design.

  2007cites this paper
• Structure based drug design for HIV protease: from molecular modeling to cheminformatics.

  2007cites this paper
• Ligand design by a combinatorial approach based on modeling and experiment: application to HLA-DR4

  2007cites this paper
• Enantiomeric separation and determination of absolute stereochemistry of asymmetric molecules in drug discovery: building chiral technology toolboxes.

  2007cites this paper
• Pharmacophore modeling in drug discovery and development: an overview.

  2007cites this paper
• Incorporating Dynamics in E. coli Dihydrofolate Reductase Enhances Structure-Based Drug Discovery

  2007cites this paper
• Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors

  2006cites this paper
• Evaluation of a neural networks QSAR method based on ligand representation using substituent descriptors. Application to HIV-1 protease inhibitors.

  2006cites this paper
• Molecular dynamics: survey of methods for simulating the activity of proteins.

  2006cites this paper
• Chapter 12 Structure-Based Lead Optimization

  2005cites this paper
• Identification of novel estrogen receptor alpha antagonists.

  2004cites this paper
• Virtual drug screening of the HIV-1 capsid protein (p24)

  2004cites this paper
• Gaussian mapping of chemical fragments in ligand binding sites

  2004cites this paper
• High-throughput docking as a source of novel drug leads.

  2004cites this paper
• SitePrint: Three-Dimensional Pharmacophore Descriptors Derived from Protein Binding Sites for Family Based Active Site Analysis, Classification, and Drug Design

  2004cites this paper
• Pharmacophore‐based molecular docking to account for ligand flexibility

  2003influential citation