History of 3D pharmacophore searching: commercial, academic and open-source tools.

The history of the evolution of the methodology to search 3D databases using pharmacophores is recounted, starting with the work of Kier 1968–1971, where he articulated the concept of a pharmacophore and laid out its role in the methodology of ‘receptor-mapping’, and ending with today's emergence of open-source tools for pharmacophore searching.

[1]  T. Langer,et al.  Pharmacophore definition and 3D searches. , 2004, Drug discovery today. Technologies.

[2]  David E. Shaw,et al.  PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results , 2006, J. Comput. Aided Mol. Des..

[3]  Douglas C. Rohrer.  3D Molecular Similarity Modelling in Computational Drug Design , 1995 .

[4]  Peter Gund,et al.  Chapter 29 Pharmacophoric Pattern Searching and Receptor Mapping , 1979 .

[5]  R. Sheridan,et al.  3DSEARCH: a system for three-dimensional substructure searching , 1989, J. Chem. Inf. Comput. Sci..

[6]  James P. Snyder,et al.  APOLLO pharmacophores and the pseudoreceptor concept , 1993 .

[7]  G. Hartman,et al.  Non‐peptide fibrinogen receptor antagonists. 41. The synthesis of [3H]L‐756,568 , 1998 .

[8]  Michael M. Mysinger,et al.  Automated Docking Screens: A Feasibility Study , 2009, Journal of medicinal chemistry.

[9]  Mark S. Johnson,et al.  Generating Conformer Ensembles Using a Multiobjective Genetic Algorithm , 2007, J. Chem. Inf. Model..

[10]  G M Crippen,et al.  Distance geometry approach to rationalizing binding data. , 1979, Journal of medicinal chemistry.

[11]  Thomas E. Moock,et al.  Conformational searching in ISIS/3D databases , 1994, J. Chem. Inf. Comput. Sci..

[12]  T. Langer.  Pharmacophores in Drug Research , 2010, Molecular informatics.

[13]  Richard Phillips Feynman,et al.  Cargo Cult Science , 1974 .

[14]  Garland R. Marshall,et al.  The Conformational Parameter in Drug Design: The Active Analog Approach , 1979 .

[15]  L B Kier,et al.  Molecular orbital calculation of preferred conformations of acetylcholine, muscarine, and muscarone. , 1967, Molecular pharmacology.

[16]  J. Gasteiger,et al.  Automatic generation of 3D-atomic coordinates for organic molecules , 1990 .

[17]  Yvonne C. Martin,et al.  ALADDIN: An integrated tool for computer-assisted molecular design and pharmacophore recognition from geometric, steric, and substructure searching of three-dimensional molecular structures , 1989, J. Comput. Aided Mol. Des..

[18]  Thomas G. Dietterich,et al.  Compass: A shape-based machine learning tool for drug design , 1994, J. Comput. Aided Mol. Des..

[19]  Ashwin Srinivasan,et al.  Pharmacophore Discovery Using the Inductive Logic Programming System PROGOL , 1998, Machine Learning.

[20]  Thierry Langer,et al.  Influenza Virus Neuraminidase Inhibitors: Generation and Comparison of Structure‐Based and Common Feature Pharmacophore Hypotheses and Their Application in Virtual Screening. , 2004 .

[21]  John H. Van Drie.  "Shrink-Wrap" Surfaces: A New Method for Incorporating Shape into Pharmacophoric 3D Database Searching , 1997, J. Chem. Inf. Comput. Sci..

[22]  Ramon Carbó.  Molecular Similarity and Reactivity , 1995 .

[23]  C. Steinbeck,et al.  Recent developments of the chemistry development kit (CDK) - an open-source java library for chemo- and bioinformatics. , 2006, Current pharmaceutical design.

[24]  Tad Hurst,et al.  Flexible 3D searching: The directed tweak technique , 1994, J. Chem. Inf. Comput. Sci..

[25]  G. Maggiora,et al.  A molecular field-based similarity approach to pharmacophoric pattern recognition. , 1997, Journal of molecular graphics & modelling.

[26]  P. Andrews,et al.  A common structural model for central nervous system drugs and their receptors. , 1986, Journal of medicinal chemistry.

[27]  Y. Martin,et al.  3D database searching in drug design. , 1992, Journal of medicinal chemistry.

[28]  Yvonne C. Martin,et al.  A fast new approach to pharmacophore mapping and its application to dopaminergic and benzodiazepine agonists , 1993, J. Comput. Aided Mol. Des..

[29]  Ajay N. Jain,et al.  Molecular Shape and Medicinal Chemistry: A Perspective , 2010, Journal of medicinal chemistry.

[30]  R J Lynch,et al.  Non-peptide fibrinogen receptor antagonists. 1. Discovery and design of exosite inhibitors. , 1992, Journal of medicinal chemistry.

[31]  Hans-Joachim Böhm,et al.  The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure , 1994, J. Comput. Aided Mol. Des..

[32]  Edward J. Lloyd,et al.  A Common Structural Model for Central Nervous System Drugs and Their Receptors. , 1986 .

[33]  Rajarshi Guha,et al.  Pharmacophore Representation and Searching , 2008 .

[34]  Yvonne C. Martin,et al.  MENTHOR, a database system for the storage and retrieval of three-dimensional molecular structures and associated data searchable by substructural, biologic, physical, or geometric properties , 1988, J. Comput. Aided Mol. Des..

[35]  S. Wold,et al.  Comparative molecular field analysis , 1991 .

[36]  J. V. Drie.  Pharmacophore Discovery: A Critical Review , 2003 .

[37]  J. S. Dixon,et al.  Distance Geometry in Molecular Modeling , 2007 .

[38]  John H. Van Drie,et al.  Strategies for the determination of pharmacophoric 3D database queries , 1997, J. Comput. Aided Mol. Des..

[39]  John H. Van Drie,et al.  Monty Kier and the Origin of the Pharmacophore Concept , 2007 .

[40]  Andrew R. Leach,et al.  WIZARD: AI in conformational analysis , 1987, J. Comput. Aided Mol. Des..

[41]  Valerie J. Gillet,et al.  Generation of multiple pharmacophore hypotheses using multiobjective optimisation techniques , 2004, J. Comput. Aided Mol. Des..

[42]  Hongma Sun,et al.  Pharmacophore-based virtual screening. , 2008, Current medicinal chemistry.

[43]  Paul A. Bartlett,et al.  CAVEAT: A program to facilitate the design of organic molecules , 1994, J. Comput. Aided Mol. Des..

[44]  R. Cramer,et al.  Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. , 1988, Journal of the American Chemical Society.

[45]  Valeriĭ Efimovich Golender,et al.  Logical and combinatorial algorithms for drug design , 1983 .

[46]  L Boulu,et al.  Voronoi receptor site models. , 1989, Progress in clinical and biological research.

[47]  H. Kubinyi.  Drug research: myths, hype and reality , 2003, Nature Reviews Drug Discovery.

[48]  John H. Van Drie.  An inequality for 3D database searching and its use in evaluating the treatment of conformational flexibility , 1996, J. Comput. Aided Mol. Des..

[49]  Thierry Langer,et al.  LigandScout: 3-D Pharmacophores Derived from Protein-Bound Ligands and Their Use as Virtual Screening Filters , 2005, J. Chem. Inf. Model..

[50]  Benjamin A. Ellingson,et al.  Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database , 2010, J. Chem. Inf. Model..

[51]  Egon L. Willighagen,et al.  Bioclipse: an open source workbench for chemo- and bioinformatics , 2007, BMC Bioinformatics.

[52]  Gabriëlle M. Donné-Op den Kelder,et al.  Distance geometry analysis of ligand binding to drug receptor sites , 1987, J. Comput. Aided Mol. Des..

[53]  Hugo Kubinyi,et al.  3D QSAR in drug design : theory, methods and applications , 2000 .

[54]  Peter Willett,et al.  Algorithms for the identification of three-dimensional maximal common substructures , 1987, J. Chem. Inf. Comput. Sci..

[55]  Gareth Jones,et al.  A genetic algorithm for flexible molecular overlay and pharmacophore elucidation , 1995, J. Comput. Aided Mol. Des..

[56]  W F van Gunsteren,et al.  Decomposition of the free energy of a system in terms of specific interactions. Implications for theoretical and experimental studies. , 1994, Journal of molecular biology.

[57]  A. Cavalli,et al.  Toward a pharmacophore for drugs inducing the long QT syndrome: insights from a CoMFA study of HERG K(+) channel blockers. , 2002, Journal of medicinal chemistry.

[58]  J. Jenkins,et al.  A 3D similarity method for scaffold hopping from known drugs or natural ligands to new chemotypes. , 2004, Journal of medicinal chemistry.

[59]  Ashwin Srinivasan,et al.  Quantitative pharmacophore models with inductive logic programming , 2006, Machine Learning.

[60]  Dorica Mayer,et al.  A unique geometry of the active site of angiotensin-converting enzyme consistent with structure-activity studies , 1987, J. Comput. Aided Mol. Des..

[61]  Richard A. Lewis,et al.  Three-dimensional pharmacophore methods in drug discovery. , 2010, Journal of medicinal chemistry.

[62]  John H. Van Drie,et al.  Pharmacophore Discovery - Lessons Learned , 2003 .