Ensemble Docking into Multiple Crystallographically Derived Protein Structures: An Evaluation Based on the Statistical Analysis of Enrichments
暂无分享,去创建一个
[1] Alison R. Gregro,et al. Discovery and SAR of isonicotinamide BACE-1 inhibitors that bind beta-secretase in a N-terminal 10s-loop down conformation. , 2007, Bioorganic & medicinal chemistry letters.
[2] Rajiv Chopra,et al. Acylguanidines as Small-Molecule β-Secretase Inhibitors , 2006 .
[3] J. Irwin,et al. ZINC ? A Free Database of Commercially Available Compounds for Virtual Screening. , 2005 .
[4] J. Gready,et al. Combining docking and molecular dynamic simulations in drug design , 2006, Medicinal research reviews.
[5] Thomas Lengauer,et al. FlexE: efficient molecular docking considering protein structure variations. , 2001, Journal of molecular biology.
[6] Claudio N. Cavasotto,et al. Protein flexibility in ligand docking and virtual screening to protein kinases. , 2004, Journal of molecular biology.
[7] X. Zou,et al. Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking , 2006, Proteins.
[8] Christopher R. Corbeil,et al. Docking Ligands into Flexible and Solvated Macromolecules, 1. Development and Validation of FITTED 1.0 , 2007, J. Chem. Inf. Model..
[9] H. Carlson. Protein flexibility and drug design: how to hit a moving target. , 2002, Current opinion in chemical biology.
[10] Woody Sherman,et al. Improving database enrichment through ensemble docking , 2008, J. Comput. Aided Mol. Des..
[11] Ajay N. Jain,et al. Recommendations for evaluation of computational methods , 2008, J. Comput. Aided Mol. Des..
[12] Yuan-Ping Pang,et al. Prediction of the binding sites of huperzine A in acetylcholinesterase by docking studies , 1994, J. Comput. Aided Mol. Des..
[13] G. McGaughey,et al. Beta-secretase (BACE-1) inhibitors: accounting for 10s loop flexibility using rigid active sites. , 2007, Bioorganic & medicinal chemistry letters.
[14] J. Irwin,et al. Benchmarking sets for molecular docking. , 2006, Journal of medicinal chemistry.
[15] I. Kuntz,et al. Molecular docking to ensembles of protein structures. , 1997, Journal of molecular biology.
[16] Xiaoqin Zou,et al. Inclusion of Solvation and Entropy in the Knowledge-Based Scoring Function for Protein-Ligand Interactions , 2010, J. Chem. Inf. Model..
[17] T. Iwatsubo,et al. Naphthyl and coumarinyl biarylpiperazine derivatives as highly potent human beta-secretase inhibitors. Design, synthesis, and enzymatic BACE-1 and cell assays. , 2006, Journal of medicinal chemistry.
[18] Min Xu,et al. Discovery of oxadiazoyl tertiary carbinamine inhibitors of beta-secretase (BACE-1). , 2006, Journal of medicinal chemistry.
[19] E. Thorsett,et al. Design and synthesis of hydroxyethylene-based peptidomimetic inhibitors of human beta-secretase. , 2004, Journal of medicinal chemistry.
[20] Xin Wen,et al. BindingDB: a web-accessible database of experimentally determined protein–ligand binding affinities , 2006, Nucleic Acids Res..
[21] M L Teodoro,et al. Conformational flexibility models for the receptor in structure based drug design. , 2003, Current pharmaceutical design.
[22] Ruben Abagyan,et al. Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking. , 2009, Journal of medicinal chemistry.
[23] R. Friesner,et al. Novel procedure for modeling ligand/receptor induced fit effects. , 2006, Journal of medicinal chemistry.
[24] M. Sternberg,et al. The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking. , 2005, Journal of molecular biology.
[25] Christopher I. Bayly,et al. Evaluating Virtual Screening Methods: Good and Bad Metrics for the "Early Recognition" Problem , 2007, J. Chem. Inf. Model..
[26] L. Kavraki,et al. On the characterization of protein native state ensembles. , 2007, Biophysical journal.
[27] A. Leach,et al. Prediction of Protein—Ligand Interactions. Docking and Scoring: Successes and Gaps , 2006 .
[28] M. Katharine Holloway,et al. BACE-1 inhibition by a series of ψ[CH2NH] reduced amide isosteres , 2006 .
[29] Ruben Abagyan,et al. A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE) , 2008, J. Comput. Aided Mol. Des..
[30] Tom Fawcett,et al. An introduction to ROC analysis , 2006, Pattern Recognit. Lett..
[31] Heather A Carlson,et al. Exploring experimental sources of multiple protein conformations in structure-based drug design. , 2007, Journal of the American Chemical Society.
[32] Martin Zacharias,et al. Energy minimization in low‐frequency normal modes to efficiently allow for global flexibility during systematic protein–protein docking , 2008, Proteins.
[33] Anthony Nicholls,et al. What do we know and when do we know it? , 2008, J. Comput. Aided Mol. Des..
[34] A. Caflisch,et al. Functional Plasticity in the Substrate Binding Site of β-Secretase , 2005 .
[35] P. Cozzini. Target Flexibility: An Emerging Consideration in Drug Discovery and Design , 2009 .
[36] X. Barril,et al. Unveiling the full potential of flexible receptor docking using multiple crystallographic structures. , 2005, Journal of medicinal chemistry.
[37] B. Shoichet,et al. Soft docking and multiple receptor conformations in virtual screening. , 2004, Journal of medicinal chemistry.
[38] Claudio N. Cavasotto,et al. Representing receptor flexibility in ligand docking through relevant normal modes. , 2005, Journal of the American Chemical Society.
[39] Joseph B. Moon,et al. Design, synthesis, and crystal structure of hydroxyethyl secondary amine-based peptidomimetic inhibitors of human beta-secretase. , 2007, Journal of medicinal chemistry.
[40] R. Abagyan,et al. Flexible ligand docking to multiple receptor conformations: a practical alternative. , 2008, Current opinion in structural biology.
[41] J. Hanley,et al. The meaning and use of the area under a receiver operating characteristic (ROC) curve. , 1982, Radiology.
[42] Robert Abel,et al. Protein side-chain dynamics and residual conformational entropy. , 2009, Journal of the American Chemical Society.
[43] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[44] Hwangseo Park,et al. Determination of the active site protonation state of beta-secretase from molecular dynamics simulation and docking experiment: implications for structure-based inhibitor design. , 2003, Journal of the American Chemical Society.
[45] Brian K Shoichet,et al. Testing a flexible-receptor docking algorithm in a model binding site. , 2004, Journal of molecular biology.
[46] Rommie E. Amaro,et al. Ensemble-Based Virtual Screening Reveals Potential Novel Antiviral Compounds for Avian Influenza Neuraminidase , 2008, Journal of medicinal chemistry.
[47] William J. Welsh,et al. Identification of a Minimal Subset of Receptor Conformations for Improved Multiple Conformation Docking and Two-Step Scoring. , 2004 .