S. A. Stein, Anne E. Loccisano, S. Firestine, J. Evanseck
{"title":"Chapter 13 Principal Components Analysis: A Review of its Application on Molecular Dynamics Data","authors":"S. A. Stein, Anne E. Loccisano, S. Firestine, J. Evanseck","doi":"10.1016/S1574-1400(06)02013-5","DOIUrl":"https://doi.org/10.1016/S1574-1400(06)02013-5","url":null,"abstract":"","PeriodicalId":88823,"journal":{"name":"Annual reports in computational chemistry","volume":"2 1","pages":"233-261"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1574-1400(06)02013-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"56635482","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Chapter 16 Recent Evaluations of High Throughput Docking Methods for Pharmaceutical Lead Finding – Consensus and Caveats","authors":"W. Cornell","doi":"10.1016/S1574-1400(06)02016-0","DOIUrl":"https://doi.org/10.1016/S1574-1400(06)02016-0","url":null,"abstract":"","PeriodicalId":88823,"journal":{"name":"Annual reports in computational chemistry","volume":"2 1","pages":"297-323"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1574-1400(06)02016-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"56635551","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Chapter 1 Real-World Kinetics via Simulations","authors":"F. A. Houle, W. Hinsberg","doi":"10.1016/S1574-1400(06)02001-9","DOIUrl":"https://doi.org/10.1016/S1574-1400(06)02001-9","url":null,"abstract":"","PeriodicalId":88823,"journal":{"name":"Annual reports in computational chemistry","volume":"2 1","pages":"3-16"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1574-1400(06)02001-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"56634912","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Andreas Bender, Jeremy L Jenkins, Qingliang Li, Sam E Adams, Edward O Cannon, Robert C Glen
{"title":"Chapter 9 Molecular Similarity: Advances in Methods, Applications and Validations in Virtual Screening and QSAR.","authors":"Andreas Bender, Jeremy L Jenkins, Qingliang Li, Sam E Adams, Edward O Cannon, Robert C Glen","doi":"10.1016/S1574-1400(06)02009-3","DOIUrl":"https://doi.org/10.1016/S1574-1400(06)02009-3","url":null,"abstract":"<p><p>This chapter discusses recent developments in some of the areas that exploit the molecular similarity principle, novel approaches to capture molecular properties by the use of novel descriptors, focuses on a crucial aspect of computational models-their validity, and discusses additional ways to examine data available, such as those from high-throughput screening (HTS) campaigns and to gain more knowledge from this data. The chapter also presents some of the recent applications of methods discussed focusing on the successes of virtual screening applications, database clustering and comparisons (such as drug- and in-house-likeness), and the recent large-scale validations of docking and scoring programs. While a great number of descriptors and modeling methods has been proposed until today, the recent trend toward proper model validation is very much appreciated. Although some of their limitations are surely because of underlying principles and limitations of fundamental concepts, others will certainly be eliminated in the future.</p>","PeriodicalId":88823,"journal":{"name":"Annual reports in computational chemistry","volume":"2 ","pages":"141-168"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1574-1400(06)02009-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37895487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Chapter 14 Solvent Effects on Organic Reactions from QM/MM Simulations","authors":"O. Acevedo, W. L. Jorgensen","doi":"10.1016/S1574-1400(06)02014-7","DOIUrl":"https://doi.org/10.1016/S1574-1400(06)02014-7","url":null,"abstract":"","PeriodicalId":88823,"journal":{"name":"Annual reports in computational chemistry","volume":"2 1","pages":"263-278"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1574-1400(06)02014-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"56635529","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Time-Dependent Density Functional Theory in Quantum Chemistry","authors":"F. Furche, K. Burke","doi":"10.1016/S1574-1400(05)01002-9","DOIUrl":"https://doi.org/10.1016/S1574-1400(05)01002-9","url":null,"abstract":"","PeriodicalId":88823,"journal":{"name":"Annual reports in computational chemistry","volume":"19 1","pages":"19-30"},"PeriodicalIF":0.0,"publicationDate":"2005-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1574-1400(05)01002-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"56635025","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Chapter 3 Computational Thermochemistry: A Brief Overview of Quantum Mechanical Approaches","authors":"Jan M. L. Martin","doi":"10.1016/S1574-1400(05)01003-0","DOIUrl":"https://doi.org/10.1016/S1574-1400(05)01003-0","url":null,"abstract":"","PeriodicalId":88823,"journal":{"name":"Annual reports in computational chemistry","volume":"1 1","pages":"31-43"},"PeriodicalIF":0.0,"publicationDate":"2005-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1574-1400(05)01003-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"56635038","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Chapter 9 Calculating Binding Free Energy in Protein–Ligand Interaction","authors":"K. Raha, K. Merz","doi":"10.1016/S1574-1400(05)01009-1","DOIUrl":"https://doi.org/10.1016/S1574-1400(05)01009-1","url":null,"abstract":"","PeriodicalId":88823,"journal":{"name":"Annual reports in computational chemistry","volume":"1 1","pages":"113-130"},"PeriodicalIF":0.0,"publicationDate":"2005-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1574-1400(05)01009-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"56635153","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}