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In: Liu LA, Wei D, Li Y, Lei H, editors. Handbook of Research on Computational and Systems Biology: Interdisciplinary Applications: IGI.","DOI":"10.4018\/978-1-60960-491-2.ch002"},{"key":"ref18","doi-asserted-by":"crossref","unstructured":"Barakat K, H, Tuszynski J (2011) Virtual Screening for DNA Repair Inhibitors. In: Storici F, editor. DNA Repair - On the Pathways to Fixing DNA Damage and Errors. 1 ed. Rijeka: InTech.","DOI":"10.5772\/24436"},{"key":"ref19","unstructured":"Chimiotheque Nationale library. <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/chimiotheque-nationale.enscm.fr\/?lang=en\" xlink:type=\"simple\">http:\/\/chimiotheque-nationale.enscm.fr\/?lang=en<\/ext-link>. 2012 Last accessed November 15."},{"key":"ref20","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1002\/(SICI)1097-0134(19990701)36:1<87::AID-PROT8>3.0.CO;2-R","article-title":"Exploring the dynamic information content of a protein NMR structure: comparison of a molecular dynamics simulation with the NMR and X-ray structures of Escherichia coli ribonuclease HI","volume":"36","author":"M Philippopoulos","year":"1999","journal-title":"Proteins"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1002\/bip.10218","article-title":"The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme","volume":"68","author":"JH Lin","year":"2003","journal-title":"Biopolymers"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"1879","DOI":"10.1021\/jm0341913","article-title":"Discovery of a novel binding trench in HIV integrase","volume":"47","author":"JR Schames","year":"2004","journal-title":"J Med Chem"},{"key":"ref23","unstructured":"Markowitz MN, Gotuzzo F, Mendo F, Ratanasuwan W, Kovacs C, <etal>et al<\/etal>.. (2006) Potent antiviral effect of MK-0518, novel HIV-1 integrase inhibitor, as part of combination ART in treatment-naive HIV-1 infected patients. 16th International AIDS Conference, Toronto, Canada."},{"key":"ref24","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1016\/j.compbiolchem.2008.12.002","article-title":"A virtual screening study of the acetylcholine binding protein using a relaxed-complex approach","volume":"33","author":"A Babakhani","year":"2009","journal-title":"Comput Biol Chem"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"17278","DOI":"10.1073\/pnas.0805820105","article-title":"Discovery of drug-like inhibitors of an essential RNA-editing ligase in Trypanosoma brucei","volume":"105","author":"RE Amaro","year":"2008","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1016\/j.compbiolchem.2010.03.005","article-title":"Potential drug-like inhibitors of Group 1 influenza neuraminidase identified through computer-aided drug design","volume":"34","author":"JD Durrant","year":"2010","journal-title":"Comput Biol Chem"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"5025","DOI":"10.1021\/jm100456a","article-title":"Computer-aided identification of Trypanosoma brucei uridine diphosphate galactose 4\u2032-epimerase inhibitors: toward the development of novel therapies for African sleeping sickness","volume":"53","author":"JD Durrant","year":"2010","journal-title":"J Med Chem"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1016\/j.jmgm.2009.12.003","article-title":"Ensemble-based virtual screening reveals dual-inhibitors for the p53-MDM2\/MDMX interactions","volume":"28","author":"K Barakat","year":"2010","journal-title":"J Mol Graph Model"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1016\/j.chembiol.2010.05.019","article-title":"Discovery and characterization of the laulimalide-microtubule binding mode by mass shift perturbation mapping","volume":"17","author":"MJ Bennett","year":"2010","journal-title":"Chem Biol"},{"key":"ref30","doi-asserted-by":"crossref","unstructured":"Barakat K, Issac B, Stepanova M, Tuszynski J (2010) Effects of temperature on the p53-DNA binding interactions and their dynamical behavior: Comparing the wild type to the R248Q mutant. 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Characterizing the Performance of Different Clustering Algorithms. Journal of Chemical Theory and Computation","volume":"3","author":"J Shao","year":"2007"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"712","DOI":"10.1002\/prot.21123","article-title":"Comparison of multiple Amber force fields and development of improved protein backbone parameters","volume":"65","author":"V Hornak","year":"2006","journal-title":"Proteins"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"1157","DOI":"10.1002\/jcc.20035","article-title":"Development and testing of a general amber force field","volume":"25","author":"J Wang","year":"2004","journal-title":"J Comput Chem"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1006\/jcph.1999.6201","article-title":"NAMD2: Greater Scalability for Parallel Molecular Dynamics","volume":"151","author":"L Kal\u00e9","year":"1999","journal-title":"Journal of Computational Physics"},{"key":"ref53"},{"key":"ref54","first-page":"135","article-title":"Chalcones et flavonones deriv\u00e9es de l\u2019acide beta-r\u00e9sorcylique. 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