Design and Diversity Analysis of Compound Libraries for Lead Discovery
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[1] I D Kuntz,et al. Structure-based design and combinatorial chemistry yield low nanomolar inhibitors of cathepsin D. , 1997, Chemistry & biology.
[2] Robert D. Clark,et al. Virtual Compound Libraries: A New Approach to Decision Making in Molecular Discovery Research , 1998, J. Chem. Inf. Comput. Sci..
[3] Paola Gramatica,et al. Weighted holistic invariant molecular descriptors. Part 2. Theory development and applications on modeling physicochemical properties of polyaromatic hydrocarbons , 1995 .
[4] John M. Barnard,et al. Clustering of chemical structures on the basis of two-dimensional similarity measures , 1992, J. Chem. Inf. Comput. Sci..
[5] Louis Hodes,et al. An Efficient Design for Chemical Structure Searching. II. The File Oraganization , 1978, J. Chem. Inf. Comput. Sci..
[6] J Alper,et al. Drug discovery on the assembly line. , 1994, Science.
[7] John M. Barnard,et al. Chemical Similarity Searching , 1998, J. Chem. Inf. Comput. Sci..
[8] Sung Jin Cho,et al. Rational design of a targeted combinatorial chemical library with opiatelike activity , 1998 .
[9] Robert D. Brown. Descriptors for diversity analysis , 1996 .
[10] 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.
[11] Michael F. Lynch,et al. Strategic Considerations in the Design of a Screening System for Substructure Searches of Chemical Structure Files , 1973 .
[12] Robin Taylor,et al. Simulation Analysis of Experimental Design Strategies for Screening Random Compounds as Potential New Drugs and Agrochemicals , 1995, J. Chem. Inf. Comput. Sci..
[13] Thomas Lengauer,et al. RigFit: A new approach to superimposing ligand molecules , 1998, German Conference on Bioinformatics.
[14] Klaus Gubernator,et al. Optimization of the Biological Activity of Combinatorial Compound Libraries by a Genetic Algorithm , 1995 .
[15] Lemont B. Kier,et al. The electrotopological state: structure information at the atomic level for molecular graphs , 1991, J. Chem. Inf. Comput. Sci..
[16] J. Gasteiger,et al. Autocorrelation of Molecular Surface Properties for Modeling Corticosteroid Binding Globulin and Cytosolic Ah Receptor Activity by Neural Networks , 1995 .
[17] G. Jung,et al. Organic Chemistry on Solid Supports , 1996 .
[18] Lutz Weber,et al. Evolutionary combinatorial chemistry: application of genetic algorithms , 1998 .
[19] A. Ghose,et al. Atomic Physicochemical Parameters for Three‐Dimensional Structure‐Directed Quantitative Structure‐Activity Relationships I. Partition Coefficients as a Measure of Hydrophobicity , 1986 .
[20] Arup K. Ghose,et al. Atomic physicochemical parameters for three dimensional structure directed quantitative structure-activity relationships. 4. Additional parameters for hydrophobic and dispersive interactions and their application for an automated superposition of certain naturally occurring nucleoside antibiotics , 1989, J. Chem. Inf. Comput. Sci..
[21] D. E. Patterson,et al. Designing Chemical Libraries for Lead Discovery , 1996 .
[22] Brian K. Shoichet,et al. Molecular docking using shape descriptors , 1992 .
[23] Wendy A. Warr,et al. Combinatorial Chemistry and Molecular Diversity. An Overview , 1997, J. Chem. Inf. Comput. Sci..
[24] G J Williams,et al. The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.
[25] Bruce L. Bush,et al. Extending the trend vector: The trend matrix and sample-based partial least squares , 1994, J. Comput. Aided Mol. Des..
[26] M. Lajiness. Dissimilarity-based compound selection techniques , 1996 .
[27] Sung Jin Cho,et al. Rational Combinatorial Library Design. 1. Focus-2D: A New Approach to the Design of Targeted Combinatorial Chemical Libraries , 1998, J. Chem. Inf. Comput. Sci..
[28] S. P. Fodor,et al. Applications of combinatorial technologies to drug discovery. 1. Background and peptide combinatorial libraries. , 1994, Journal of medicinal chemistry.
[29] Johann Gasteiger,et al. Assessing Similarity and Diversity of Combinatorial Libraries by Spatial Autocorrelation Functions and Neural Networks , 1996 .
[30] Robert D Clark,et al. Bioisosterism as a molecular diversity descriptor: steric fields of single "topomeric" conformers. , 1996, Journal of medicinal chemistry.
[31] Thomas Lengauer,et al. Multiple automatic base selection: Protein–ligand docking based on incremental construction without manual intervention , 1997, J. Comput. Aided Mol. Des..
[32] Ajay,et al. Can we learn to distinguish between "drug-like" and "nondrug-like" molecules? , 1998, Journal of medicinal chemistry.
[33] David M. Rocke,et al. Predicting ligand binding to proteins by affinity fingerprinting. , 1995, Chemistry & biology.
[34] Robert P. Sheridan,et al. Chemical Similarity Using Geometric Atom Pair Descriptors , 1996, J. Chem. Inf. Comput. Sci..
[35] P. Willett,et al. A Comparison of Some Measures for the Determination of Inter‐Molecular Structural Similarity Measures of Inter‐Molecular Structural Similarity , 1986 .
[36] Robert D. Clark,et al. Balancing Representativeness Against Diversity using Optimizable K-Dissimilarity and Hierarchical Clustering , 1998, J. Chem. Inf. Comput. Sci..
[37] John H. Van Drie,et al. Approaches to virtual library design , 1998 .
[38] Stephen D. Pickett,et al. Diversity Profiling and Design Using 3D Pharmacophores: Pharmacophore-Derived Queries (PDQ) , 1996, J. Chem. Inf. Comput. Sci..
[39] R. Venkataraghavan,et al. Atom pairs as molecular features in structure-activity studies: definition and applications , 1985, J. Chem. Inf. Comput. Sci..
[40] Yvonne C. Martin,et al. Use of Structure-Activity Data To Compare Structure-Based Clustering Methods and Descriptors for Use in Compound Selection , 1996, J. Chem. Inf. Comput. Sci..
[41] Gnther Jung,et al. Combinatorial Peptide and Nonpeptide Libraries , 1996 .
[42] Bohdan Waszkowycz,et al. Targeted molecular diversity in drug discovery: Integration of structure-based design and combinatorial chemistry , 1998 .
[43] 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..
[44] Louis Hodes,et al. Selection of Descriptors According to Discrimination and Redundancy. Application to Chemical Structure Searching , 1976, J. Chem. Inf. Comput. Sci..
[45] S. P. Fodor,et al. Applications of combinatorial technologies to drug discovery. 2. Combinatorial organic synthesis, library screening strategies, and future directions. , 1994, Journal of medicinal chemistry.
[46] Mark A. Murcko,et al. Virtual screening : an overview , 1998 .
[47] W. DeGrado,et al. Complementarity of Combinatorial Chemistry and Structure-Based Ligand Design: Application to the Discovery of Novel Inhibitors of Matrix Metalloproteinases , 1996 .
[48] S. Wold,et al. Multivariate Data Analysis in Chemistry , 1984 .
[49] P. Willett,et al. A Fast Algorithm For Selecting Sets Of Dissimilar Molecules From Large Chemical Databases , 1995 .
[50] James B. Dunbar,et al. Enhancing the diversity of a corporate database using chemical database clustering and analysis , 1995, J. Comput. Aided Mol. Des..
[51] W. Moos,et al. The generation of molecular diversity , 1993 .
[52] Hans-Joachim Böhm,et al. Prediction of binding constants of protein ligands: A fast method for the prioritization of hits obtained from de novo design or 3D database search programs , 1998, J. Comput. Aided Mol. Des..
[53] Peter G. Schultz,et al. A Structure-Based Library Approach to Kinase Inhibitors , 1996 .
[54] Jonathan A. Ellman,et al. Synthesis and Applications of Small Molecule Libraries. , 1996, Chemical reviews.
[55] Steven L. Teig,et al. Chemical Function Queries for 3D Database Search , 1994, J. Chem. Inf. Comput. Sci..
[56] Michael M. Hann,et al. RECAP-Retrosynthetic Combinatorial Analysis Procedure: A Powerful New Technique for Identifying Privileged Molecular Fragments with Useful Applications in Combinatorial Chemistry , 1998, J. Chem. Inf. Comput. Sci..
[57] Garland R. Marshall,et al. VALIDATE: A New Method for the Receptor-Based Prediction of Binding Affinities of Novel Ligands , 1996 .
[58] Darren R. Flower,et al. On the Properties of Bit String-Based Measures of Chemical Similarity , 1998, J. Chem. Inf. Comput. Sci..
[59] Ramaswamy Nilakantan,et al. Database diversity assessment: New ideas, concepts, and tools , 1997, J. Comput. Aided Mol. Des..
[60] Thomas Lengauer,et al. A fast flexible docking method using an incremental construction algorithm. , 1996, Journal of molecular biology.
[61] Gareth Jones,et al. A genetic algorithm for flexible molecular overlay and pharmacophore elucidation , 1995, J. Comput. Aided Mol. Des..
[62] David Chapman,et al. The measurement of molecular diversity: A three-dimensional approach , 1996, J. Comput. Aided Mol. Des..
[63] 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..
[64] Dinesh V. Patel,et al. Strategy and Tactics in Combinatorial Organic Synthesis. Applications to Drug Discovery , 1996 .
[65] M. Lebl,et al. Synthetic combinatorial libraries: Views on techniques and their application , 1995 .
[66] Diana C. Roe,et al. BUILDER v.2: Improving the chemistry of a de novo design strategy , 1995, J. Comput. Aided Mol. Des..
[67] Y. Martin,et al. Computational methods in molecular diversity and combinatorial chemistry. , 1998, Current opinion in chemical biology.
[68] I. Kuntz,et al. Automated docking with grid‐based energy evaluation , 1992 .
[69] Irwin D. Kuntz,et al. Automated flexible ligand docking method and its application for database search , 1997 .
[70] G. Rishton. Reactive compounds and in vitro false positives in HTS , 1997 .
[71] G. V. Paolini,et al. Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes , 1997, J. Comput. Aided Mol. Des..
[72] Sung Jin Cho,et al. Rational Combinatorial Library Design. 2. Rational Design of Targeted Combinatorial Peptide Libraries Using Chemical Similarity Probe and the Inverse QSAR Approaches , 1998, J. Chem. Inf. Comput. Sci..
[73] R. Everett. Analysis and modeling of fiber clustering in composites using N-tuples , 1993 .
[74] P. Willett,et al. Implementation of nonhierarchic cluster analysis methods in chemical information structure search , 1986 .
[75] R. Houghten,et al. The Current Status of Heterocyclic Combinatorial Libraries. , 1997, Chemical reviews.
[76] Robert D Clark,et al. Neighborhood behavior: a useful concept for validation of "molecular diversity" descriptors. , 1996, Journal of medicinal chemistry.
[77] H Matter,et al. Random or rational design? Evaluation of diverse compound subsets from chemical structure databases. , 1998, Journal of medicinal chemistry.
[78] Ajay N. Jain. Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities , 1996, J. Comput. Aided Mol. Des..
[79] Vijay K. Gombar,et al. Quantitative Structure‐Activity Relationship (QSAR) Studies Using Electronic Descriptors Calculated from Topological and Molecular Orbital (MO) Methods , 1990 .
[80] Paola Gramatica,et al. Modeling and prediction by using WHIM descriptors in QSAR studies: submitochondrial particles (SMP) as toxicity blosensors of chlorophenols , 1996 .
[81] Marina Lasagni,et al. New molecular descriptors for 2D and 3D structures. Theory , 1994 .
[82] Malcolm J. McGregor,et al. Clustering of Large Databases of Compounds: Using the MDL "Keys" as Structural Descriptors , 1997, J. Chem. Inf. Comput. Sci..
[83] J. Mason,et al. New perspectives in lead generation II: Evaluating molecular diversity , 1996 .
[84] Jonathan A. Ellman,et al. Design, Synthesis, and Evaluation of Small-Molecule Libraries , 1996 .
[85] A. Good,et al. New methodology for profiling combinatorial libraries and screening sets: cleaning up the design process with HARPick. , 1997, Journal of medicinal chemistry.
[86] P Willett,et al. Comparison of algorithms for dissimilarity-based compound selection. , 1997, Journal of molecular graphics & modelling.
[87] Garland R. Marshall,et al. 3D-QSAR of angiotensin-converting enzyme and thermolysin inhibitors: A comparison of CoMFA models based on deduced and experimentally determined active site geometries , 1993 .
[88] G. Bemis,et al. The properties of known drugs. 1. Molecular frameworks. , 1996, Journal of medicinal chemistry.
[89] Robert D. Clark,et al. OptiSim: An Extended Dissimilarity Selection Method for Finding Diverse Representative Subsets , 1997, J. Chem. Inf. Comput. Sci..
[90] Y. Martin,et al. Designing combinatorial library mixtures using a genetic algorithm. , 1997, Journal of medicinal chemistry.
[91] S. Wold,et al. A PLS kernel algorithm for data sets with many variables and fewer objects. Part 1: Theory and algorithm , 1994 .
[92] R. Webster Homer,et al. SYBYL Line Notation (SLN): A Versatile Language for Chemical Structure Representation , 1997, J. Chem. Inf. Comput. Sci..
[93] C. Zechel,et al. Combinatorial Synthesis of Small Organic Molecules , 1996 .
[94] J. Ellman,et al. Chapter 31. Solid-Phase Synthesis: Applications to Combinatorial Libraries , 1996 .
[95] Yvonne C. Martin,et al. The Information Content of 2D and 3D Structural Descriptors Relevant to Ligand-Receptor Binding , 1997, J. Chem. Inf. Comput. Sci..
[96] Hualiang Jiang,et al. A New Approach to Design Virtual Combinatorial Library with Genetic Algorithm Based on 3D Grid Property , 1998, J. Chem. Inf. Comput. Sci..
[97] John Bradshaw,et al. The Effectiveness of Reactant Pools for Generating Structurally-Diverse Combinatorial Libraries , 1997, J. Chem. Inf. Comput. Sci..
[98] H. Kubinyi,et al. A scoring scheme for discriminating between drugs and nondrugs. , 1998, Journal of medicinal chemistry.
[99] Richard D. Cramer,et al. Solution Phase Synthesis of Chemical Libraries for Lead Discovery , 1996 .
[100] Robert P. Sheridan,et al. Chemical Similarity Using Physiochemical Property Descriptors , 1996, J. Chem. Inf. Comput. Sci..
[101] I. Kuntz,et al. Molecular similarity based on DOCK-generated fingerprints. , 1996, Journal of medicinal chemistry.
[102] L. Kier. Indexes of molecular shape from chemical graphs , 1987, Medicinal research reviews.
[103] D C Spellmeyer,et al. Measuring diversity: experimental design of combinatorial libraries for drug discovery. , 1995, Journal of medicinal chemistry.
[104] Michael F. Lynch,et al. An Evaluation of a Substructure Search Screen System Based on Bond-Centered Fragments. , 1974 .
[105] Iain M. McLay,et al. Similarity Measures for Rational Set Selection and Analysis of Combinatorial Libraries: The Diverse Property-Derived (DPD) Approach , 1997, Journal of chemical information and computer sciences.
[106] J M Blaney,et al. A geometric approach to macromolecule-ligand interactions. , 1982, Journal of molecular biology.
[107] Matthias Rarey,et al. Feature trees: A new molecular similarity measure based on tree matching , 1998, J. Comput. Aided Mol. Des..
[108] Peter Willett,et al. Similarity Searching in Files of Three-Dimensional Chemical Structures. Alignment of Molecular Electrostatic Potential Fields with a Genetic Algorithm , 1996, J. Chem. Inf. Comput. Sci..