Fragment-Based de Novo Ligand Design by Multiobjective Evolutionary Optimization
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[1] Jeffrey Horn,et al. Handbook of evolutionary computation , 1997 .
[2] Julian Tirado-Rives,et al. Computer-aided design of non-nucleoside inhibitors of HIV-1 reverse transcriptase. , 2006, Bioorganic & medicinal chemistry letters.
[3] Brian K. Shoichet,et al. ZINC - A Free Database of Commercially Available Compounds for Virtual Screening , 2005, J. Chem. Inf. Model..
[4] Petra Schneider,et al. De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks , 2000, J. Comput. Aided Mol. Des..
[5] C. Darwin. Charles Darwin The Origin of Species by means of Natural Selection or The Preservation of Favoured Races in the Struggle for Life , 2004 .
[6] A. Caflisch,et al. Fragment-Based Flexible Ligand Docking by Evolutionary Optimization , 2001, Biological chemistry.
[7] Anne Brindle,et al. Genetic algorithms for function optimization , 1980 .
[8] 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..
[9] Irwin D. Kuntz,et al. A genetic algorithm for structure-based de novo design , 2001, J. Comput. Aided Mol. Des..
[10] G. Labesse,et al. LEA3D: a computer-aided ligand design for structure-based drug design. , 2005, Journal of medicinal chemistry.
[11] Uli Fechner,et al. Flux (2): Comparison of Molecular Mutation and Crossover Operators for Ligand-Based de Novo Design. , 2007 .
[12] H. M. Vinkers,et al. SYNOPSIS: SYNthesize and OPtimize System in Silico. , 2003, Journal of medicinal chemistry.
[13] Kirsch,et al. Virtual Screening for Bioactive Molecules by Evolutionary De Novo Design Special thanks to Neil R. Taylor for his help in preparation of the manuscript. , 2000, Angewandte Chemie.
[14] P. Toogood. Cyclin‐dependent kinase inhibitors for treating cancer , 2001, Medicinal research reviews.
[15] Egon L. Willighagen,et al. The Blue Obelisk—Interoperability in Chemical Informatics , 2006, J. Chem. Inf. Model..
[16] G. Bemis,et al. Properties of known drugs. 2. Side chains. , 1999, Journal of medicinal chemistry.
[17] F. Momany,et al. Validation of the general purpose QUANTA ®3.2/CHARMm® force field , 1992 .
[18] J. Gasteiger,et al. FROM ATOMS AND BONDS TO THREE-DIMENSIONAL ATOMIC COORDINATES : AUTOMATIC MODEL BUILDERS , 1993 .
[19] W. Im,et al. Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation , 1998 .
[20] Amedeo Caflisch,et al. Efficient evaluation of binding free energy using continuum electrostatics solvation. , 2004, Journal of medicinal chemistry.
[21] Gisbert Schneider,et al. Flux (2): Comparison of Molecular Mutation and Crossover Operators for Ligand-Based de Novo Design , 2007, J. Chem. Inf. Model..
[22] G. Bemis,et al. The properties of known drugs. 1. Molecular frameworks. , 1996, Journal of medicinal chemistry.
[23] B Coupez,et al. Docking and scoring--theoretically easy, practically impossible? , 2006, Current medicinal chemistry.
[24] A Caflisch,et al. Computational ligand design. , 1999, Combinatorial chemistry & high throughput screening.
[25] Eugene I. Shakhnovich,et al. SMOG : DE NOVO DESIGN METHOD BASED ON SIMPLE, FAST, AND ACCURATE FREE ENERGY ESTIMATES. 2. CASE STUDIES IN MOLECULAR DESIGN , 1997 .
[26] Harold A. Scheraga,et al. Determination of net atomic charges using a modified partial equalization of orbital electronegativity method. 1. Application to neutral molecules as models for polypeptides , 1990 .
[27] Simon K. Kearsley,et al. An alternative method for the alignment of molecular structures: Maximizing electrostatic and steric overlap , 1990 .
[28] John H. Holland,et al. Adaptation in Natural and Artificial Systems: An Introductory Analysis with Applications to Biology, Control, and Artificial Intelligence , 1992 .
[29] N. Metropolis,et al. Equation of State Calculations by Fast Computing Machines , 1953, Resonance.
[30] A. Bennett. The Origin of Species by means of Natural Selection; or the Preservation of Favoured Races in the Struggle for Life , 1872, Nature.
[31] M. Karplus,et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .
[32] Philip M. Dean,et al. Evaluation of a method for controlling molecular scaffold diversity in de novo ligand design , 1997, J. Comput. Aided Mol. Des..
[33] Amedeo Caflisch,et al. Computational combinatorial ligand design: Application to human α-thrombin , 1996, J. Comput. Aided Mol. Des..
[34] Peter Ertl,et al. Cheminformatics Analysis of Organic Substituents: Identification of the Most Common Substituents, Calculation of Substituent Properties, and Automatic Identification of Drug-like Bioisosteric Groups , 2003, J. Chem. Inf. Comput. Sci..
[35] Anthony Williams,et al. Generation and Selection of Novel Estrogen Receptor Ligands Using the De Novo Structure-Based Design Tool, SkelGen , 2006, J. Chem. Inf. Model..
[36] Paul Bryant Grosso,et al. Computer Simulations of Genetic Adaptation: Parallel Subcomponent Interaction in a Multilocus Model , 1985 .
[37] Hans-Joachim Böhm,et al. Combinatorial docking and combinatorial chemistry: Design of potent non-peptide thrombin inhibitors , 1999, J. Comput. Aided Mol. Des..
[38] Sergio H. Rotstein,et al. GroupBuild: a fragment-based method for de novo drug design , 1994 .
[39] Gisbert Schneider,et al. Computer-based de novo design of drug-like molecules , 2005, Nature Reviews Drug Discovery.
[40] P. A. Harris,et al. Oxindole-based inhibitors of cyclin-dependent kinase 2 (CDK2): design, synthesis, enzymatic activities, and X-ray crystallographic analysis. , 2001, Journal of medicinal chemistry.
[41] Fred W. Glover,et al. Future paths for integer programming and links to artificial intelligence , 1986, Comput. Oper. Res..
[42] Fred Glover,et al. Tabu Search - Part II , 1989, INFORMS J. Comput..
[43] Luhua Lai,et al. LigBuilder: A Multi-Purpose Program for Structure-Based Drug Design , 2000 .
[44] Valerie J. Gillet,et al. SPROUT, HIPPO and CAESA: Tools for de novo structure generation and estimation of synthetic accessibility , 1995 .
[45] L. Johnson,et al. Probing the ATP ribose-binding domain of cyclin-dependent kinases 1 and 2 with O(6)-substituted guanine derivatives. , 2002, Journal of medicinal chemistry.
[46] Gisbert Schneider,et al. Identification of novel cannabinoid receptor ligands via evolutionary de novo design and rapid parallel synthesis , 2004 .
[47] J. Apostolakis,et al. Exhaustive docking of molecular fragments with electrostatic solvation , 1999, Proteins.
[48] David E. Goldberg,et al. Genetic Algorithms in Search Optimization and Machine Learning , 1988 .
[49] A. Caflisch,et al. Automatic and efficient decomposition of two-dimensional structures of small molecules for fragment-based high-throughput docking. , 2006, Journal of medicinal chemistry.
[50] Peter Kolb,et al. Discovery of kinase inhibitors by high-throughput docking and scoring based on a transferable linear interaction energy model. , 2008, Journal of medicinal chemistry.
[51] F. Lombardo,et al. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings , 1997 .
[52] Anthony Williams,et al. Exhaustive de novo Design of Low-Molecular-Weight Fragments Against the ATP-Binding Site of DNA-Gyrase , 2006, J. Chem. Inf. Model..