Computer-aided drug design: lead discovery and optimization.
暂无分享,去创建一个
Yu Cao | Wenjie Fan | Yirong Mo | Lijuan Chen | Mingli Xiang | Yu Cao | Y. Mo | Mingli Xiang | Li-juan Chen | Wenjie Fan
[1] Woody Sherman,et al. Computational approaches for fragment-based and de novo design. , 2010, Current topics in medicinal chemistry.
[2] Gisbert Schneider,et al. The concept of template-based de novo design from drug-derived molecular fragments and its application to TAR RNA , 2008, J. Comput. Aided Mol. Des..
[3] Weiliang Zhu,et al. New technologies in computer-aided drug design: Toward target identification and new chemical entity discovery , 2006, Drug Discovery Today: Technologies.
[4] Prasad V Bharatam,et al. Modelling and informatics in the analysis of P. falciparum DHFR enzyme inhibitors. , 2008, Current medicinal chemistry.
[5] M. Gleeson,et al. Theoretical analysis of peptidyl alpha-ketoheterocyclic inhibitors of human neutrophil elastase: Insight into the mechanism of inhibition and the application of QM/MM calculations in structure-based drug design. , 2004, Organic & biomolecular chemistry.
[6] Yang Zhang. Progress and challenges in protein structure prediction. , 2008, Current opinion in structural biology.
[7] Ruth Nussinov,et al. Predicting molecular interactions in silico: II. Protein-protein and protein-drug docking. , 2003 .
[8] Torsten Schwede,et al. The SWISS-MODEL Repository and associated resources , 2008, Nucleic Acids Res..
[9] Qian Liu,et al. Tagged fragment method for evolutionary structure-based de novo lead generation and optimization. , 2007, Journal of medicinal chemistry.
[10] Alexander D. MacKerell,et al. Computational identification of inhibitors of protein-protein interactions. , 2007, Current topics in medicinal chemistry.
[11] Hans-Joachim Böhm,et al. The computer program LUDI: A new method for the de novo design of enzyme inhibitors , 1992, J. Comput. Aided Mol. Des..
[12] Philip M. Dean,et al. A validation study on the practical use of automated de novo design , 2002, J. Comput. Aided Mol. Des..
[13] Hongma Sun,et al. Pharmacophore-based virtual screening. , 2008, Current medicinal chemistry.
[14] Johann Gasteiger,et al. De novo design and synthetic accessibility , 2007, J. Comput. Aided Mol. Des..
[15] Jans H Alzate-Morales,et al. A computational study of the protein-ligand interactions in CDK2 inhibitors: using quantum mechanics/molecular mechanics interaction energy as a predictor of the biological activity. , 2007, Biophysical journal.
[16] Rommie E. Amaro,et al. Emerging methods for ensemble-based virtual screening. , 2010, Current topics in medicinal chemistry.
[17] Daniel Vitt,et al. Virtual high-throughput in silico screening , 2003 .
[18] G. Klebe,et al. Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors. , 2002, Angewandte Chemie.
[19] William L Jorgensen,et al. Efficient drug lead discovery and optimization. , 2009, Accounts of chemical research.
[20] Pedro Alexandrino Fernandes,et al. Protein–ligand docking: Current status and future challenges , 2006, Proteins.
[21] S. Shaikh,et al. From drug target to leads--sketching a physicochemical pathway for lead molecule design in silico. , 2007, Current pharmaceutical design.
[22] Lochana C. Menikarachchi,et al. QM/MM approaches in medicinal chemistry research. , 2010, Current topics in medicinal chemistry.
[23] D. M. Ryan,et al. Rational design of potent sialidase-based inhibitors of influenza virus replication , 1993, Nature.
[24] R. Abagyan,et al. Comprehensive identification of "druggable" protein ligand binding sites. , 2004, Genome informatics. International Conference on Genome Informatics.
[25] Vishal Prakash Zambre,et al. Development of predictive pharmacophore model for in silico screening, and 3D QSAR CoMFA and CoMSIA studies for lead optimization, for designing of potent tumor necrosis factor alpha converting enzyme inhibitors , 2010, J. Comput. Aided Mol. Des..
[26] J. A. Grant,et al. Gaussian docking functions. , 2003, Biopolymers.
[27] G. S. Chen,et al. Novel lead generation through hypothetical pharmacophore three-dimensional database searching: discovery of isoflavonoids as nonsteroidal inhibitors of rat 5 alpha-reductase. , 2001, Journal of medicinal chemistry.
[28] Brian K Shoichet,et al. Prediction of protein-ligand interactions. Docking and scoring: successes and gaps. , 2006, Journal of medicinal chemistry.
[29] M. Field,et al. A Generalized Hybrid Orbital (GHO) Method for the Treatment of Boundary Atoms in Combined QM/MM Calculations , 1998 .
[30] Yuan-Ping Pang,et al. EUDOC: a computer program for identification of drug interaction sites in macromolecules and drug leads from chemical databases , 2001, J. Comput. Chem..
[31] C. Grütter,et al. Structural insights into how irreversible inhibitors can overcome drug resistance in EGFR. , 2008, Bioorganic & medicinal chemistry.
[32] W. Howe,et al. Computer design of bioactive molecules: A method for receptor‐based de novo ligand design , 1991, Proteins.
[33] B. McConkey,et al. The performance of current methods in ligand-protein docking , 2002 .
[34] W. Richards,et al. Identification of ligand binding sites on proteins using a multi-scale approach. , 2002, Journal of the American Chemical Society.
[35] Amedeo Caflisch,et al. Fragment-Based de Novo Ligand Design by Multiobjective Evolutionary Optimization , 2008, J. Chem. Inf. Model..
[36] J. Gready,et al. Combining docking and molecular dynamic simulations in drug design , 2006, Medicinal research reviews.
[37] Tudor I. Oprea,et al. Integrating virtual screening in lead discovery. , 2004, Current opinion in chemical biology.
[38] Julian Tirado-Rives,et al. Computer-aided design of non-nucleoside inhibitors of HIV-1 reverse transcriptase. , 2006, Bioorganic & medicinal chemistry letters.
[39] Thierry Langer,et al. Discovery of nonsteroidal 17beta-hydroxysteroid dehydrogenase 1 inhibitors by pharmacophore-based screening of virtual compound libraries. , 2008, Journal of medicinal chemistry.
[40] Whanchul Shin,et al. Binary image representation of a ligand binding site: its application to efficient sampling of a conformational ensemble , 2010, BMC Bioinformatics.
[41] Young‐Tae Chang,et al. Tools for target identification and validation. , 2004, Current opinion in chemical biology.
[42] Alexander D. MacKerell,et al. Binding Response: A Descriptor for Selecting Ligand Binding Site on Protein Surfaces , 2007, J. Chem. Inf. Model..
[43] J M Blaney,et al. A geometric approach to macromolecule-ligand interactions. , 1982, Journal of molecular biology.
[44] 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..
[45] K. Chou,et al. Progress in computational approach to drug development against SARS. , 2006, Current medicinal chemistry.
[46] Walter Thiel,et al. QM/MM methods for biomolecular systems. , 2009, Angewandte Chemie.
[47] A. Wissner,et al. The Development of HKI‐272 and Related Compounds for the Treatment of Cancer , 2008, Archiv der Pharmazie.
[48] S. Moro,et al. Novel strategies for the design of new potent and selective human A3 receptor antagonists: an update. , 2006, Current medicinal chemistry.
[49] D. Boschelli,et al. 4-Anilino-6,7-dialkoxyquinoline-3-carbonitrile inhibitors of epidermal growth factor receptor kinase and their bioisosteric relationship to the 4-anilino-6,7-dialkoxyquinazoline inhibitors. , 2000, Journal of medicinal chemistry.
[50] Alessandra Magistrato,et al. Modeling anticancer drug-DNA interactions via mixed QM/MM molecular dynamics simulations. , 2006, Organic & biomolecular chemistry.
[51] M. T. Barakat,et al. The atom assignment problem in automated de novo drug design. 4. Tests for site-directed fragment placement based on molecular complementarity , 1995, J. Comput. Aided Mol. Des..
[52] Yongqiang Zhu,et al. Pharmacophore based drug design approach as a practical process in drug discovery. , 2010, Current computer-aided drug design.
[53] P Willett,et al. Development and validation of a genetic algorithm for flexible docking. , 1997, Journal of molecular biology.
[54] Richard H. Henchman,et al. Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy. , 2004, Biophysical journal.
[55] R. Friesner. Combined quantum and molecular mechanics (QM/MM). , 2004, Drug discovery today. Technologies.
[56] Scott Myers,et al. Drug discovery—an operating model for a new era , 2001, Nature Biotechnology.
[57] W. L. Jorgensen. The Many Roles of Computation in Drug Discovery , 2004, Science.
[58] György M Keseru,et al. Hit discovery and hit-to-lead approaches. , 2006, Drug discovery today.
[59] Irwin D. Kuntz,et al. A genetic algorithm for structure-based de novo design , 2001, J. Comput. Aided Mol. Des..
[60] G. Labesse,et al. LEA3D: a computer-aided ligand design for structure-based drug design. , 2005, Journal of medicinal chemistry.
[61] M. Murcko,et al. GroupBuild: a fragment-based method for de novo drug design. , 1993, Journal of medicinal chemistry.
[62] Alexander D. MacKerell,et al. Development of extracellular signal-regulated kinase inhibitors. , 2009, Current topics in medicinal chemistry.
[63] Valerie J. Gillet,et al. Knowledge-Based Approach to de Novo Design Using Reaction Vectors , 2009, J. Chem. Inf. Model..
[64] Osman F Güner,et al. History and evolution of the pharmacophore concept in computer-aided drug design. , 2002, Current topics in medicinal chemistry.
[65] Ping-Chiang Lyu,et al. Generation of ligand-based pharmacophore model and virtual screening for identification of novel tubulin inhibitors with potent anticancer activity. , 2009, Journal of medicinal chemistry.
[66] A. Sali,et al. Protein Structure Prediction and Structural Genomics , 2001, Science.
[67] Gisbert Schneider,et al. Computer-based de novo design of drug-like molecules , 2005, Nature Reviews Drug Discovery.
[68] Thomas Lengauer,et al. Protein Structure Prediction Methods for Drug Design , 2000, Briefings Bioinform..
[69] François Durant,et al. Structure-based pharmacophore of COX-2 selective inhibitors and identification of original lead compounds from 3D database searching method. , 2006, European journal of medicinal chemistry.
[70] M. Erion,et al. Computer-aided drug design strategies used in the discovery of fructose 1, 6-bisphosphatase inhibitors. , 2005, Current pharmaceutical design.
[71] Xing-Jie Liang,et al. Therapeutic strategies underpinning the development of novel techniques for the treatment of HIV infection. , 2010, Drug discovery today.
[72] J. Åqvist,et al. The linear interaction energy method for predicting ligand binding free energies. , 2001, Combinatorial chemistry & high throughput screening.
[73] Bernard Pirard,et al. Insight into the structural determinants for selective inhibition of matrix metalloproteinases. , 2007, Drug discovery today.
[74] Sheng-Yong Yang,et al. PhDD: a new pharmacophore-based de novo design method of drug-like molecules combined with assessment of synthetic accessibility. , 2010, Journal of molecular graphics & modelling.
[75] Julian Tirado-Rives,et al. Molecular modeling of organic and biomolecular systems using BOSS and MCPRO , 2005, J. Comput. Chem..
[76] R. Nilakantan,et al. Syntheses and EGFR and HER-2 kinase inhibitory activities of 4-anilinoquinoline-3-carbonitriles: analogues of three important 4-anilinoquinazolines currently undergoing clinical evaluation as therapeutic antitumor agents. , 2002, Bioorganic & medicinal chemistry letters.
[77] A. Lesk,et al. The relation between the divergence of sequence and structure in proteins. , 1986, The EMBO journal.
[78] J. Skolnick,et al. A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation , 2008, Proceedings of the National Academy of Sciences.
[79] Y. Pang,et al. In Silico Drug Discovery: Solving the “Target‐rich and Lead‐poor” Imbalance Using the Genome‐to‐drug‐lead Paradigm , 2006, Clinical pharmacology and therapeutics.
[80] I. Kuntz. Structure-Based Strategies for Drug Design and Discovery , 1992, Science.
[81] Amedeo Caflisch,et al. Quantum mechanical methods for drug design. , 2010, Current topics in medicinal chemistry.
[82] M. Sliwkowski,et al. Structure of the Epidermal Growth Factor Receptor Kinase Domain Alone and in Complex with a 4-Anilinoquinazoline Inhibitor* , 2002, The Journal of Biological Chemistry.
[83] Markus Hartenfeller,et al. Concept of Combinatorial De Novo Design of Drug‐like Molecules by Particle Swarm Optimization , 2008, Chemical biology & drug design.
[84] Todd J. A. Ewing,et al. DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases , 2001, J. Comput. Aided Mol. Des..
[85] Sheng-Yong Yang,et al. Pharmacophore modeling and applications in drug discovery: challenges and recent advances. , 2010, Drug discovery today.
[86] B. Meunier,et al. Hybrid molecules with a dual mode of action: dream or reality? , 2008, Accounts of chemical research.
[87] Bingding Huang,et al. MetaPocket: a meta approach to improve protein ligand binding site prediction. , 2009, Omics : a journal of integrative biology.
[88] C. Shekhar. In silico pharmacology: computer-aided methods could transform drug development. , 2008, Chemistry & biology.
[89] F. Ooms,et al. Molecular modeling and computer aided drug design. Examples of their applications in medicinal chemistry. , 2000, Current medicinal chemistry.
[90] K. Lam,et al. New approaches in identifying drugs to inactivate oncogene products. , 2004, Seminars in cancer biology.
[91] B. G. Rao,et al. Recent developments in the design of specific Matrix Metalloproteinase inhibitors aided by structural and computational studies. , 2005, Current pharmaceutical design.
[92] B. Shoichet,et al. Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B. , 2002, Journal of medicinal chemistry.
[93] Peter A. Kollman,et al. FREE ENERGY CALCULATIONS : APPLICATIONS TO CHEMICAL AND BIOCHEMICAL PHENOMENA , 1993 .
[94] Teruki Honma,et al. Recent advances in de novo design strategy for practical lead identification , 2003, Medicinal research reviews.
[95] Ruth Nussinov,et al. Predicting molecular interactions in silico: I. A guide to pharmacophore identification and its applications to drug design. , 2004, Current medicinal chemistry.
[96] Robert P. Sheridan,et al. Comparison of Topological, Shape, and Docking Methods in Virtual Screening , 2007, J. Chem. Inf. Model..
[97] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[98] E. Jaeger,et al. Docking: successes and challenges. , 2005, Current pharmaceutical design.
[99] Richard A. Lewis. A general method for exploiting QSAR models in lead optimization. , 2005, Journal of medicinal chemistry.
[100] Thierry Langer,et al. Molecule-pharmacophore superpositioning and pattern matching in computational drug design. , 2008, Drug discovery today.