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Chapter 1 Free Energies of Lipid–Lipid Interactions in Membranes 第一章膜中脂质相互作用的自由能
Annual reports in computational chemistry Pub Date : 2009-01-01 DOI: 10.1016/S1574-1400(09)00501-5
W. Bennett, D. Tieleman, Daniel M. Zuckerman, R. Pappu, Dominika Zgid
{"title":"Chapter 1 Free Energies of Lipid–Lipid Interactions in Membranes","authors":"W. Bennett, D. Tieleman, Daniel M. Zuckerman, R. Pappu, Dominika Zgid","doi":"10.1016/S1574-1400(09)00501-5","DOIUrl":"https://doi.org/10.1016/S1574-1400(09)00501-5","url":null,"abstract":"","PeriodicalId":88823,"journal":{"name":"Annual reports in computational chemistry","volume":"5 1","pages":"3-21"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1574-1400(09)00501-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"56635985","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}
引用次数: 1
Chapter 8 Electron Transfer in Gaseous Positively Charged Peptides — Relation to Mass Spectrometry 第八章气态正电荷多肽中的电子转移-与质谱的关系
Annual reports in computational chemistry Pub Date : 2009-01-01 DOI: 10.1016/S1574-1400(09)00508-8
J. Simons
{"title":"Chapter 8 Electron Transfer in Gaseous Positively Charged Peptides — Relation to Mass Spectrometry","authors":"J. Simons","doi":"10.1016/S1574-1400(09)00508-8","DOIUrl":"https://doi.org/10.1016/S1574-1400(09)00508-8","url":null,"abstract":"","PeriodicalId":88823,"journal":{"name":"Annual reports in computational chemistry","volume":"5 1","pages":"163-183"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1574-1400(09)00508-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"56636050","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}
引用次数: 3
Chapter 5 Recent Advances on in silico ADME Modeling 第五章计算机ADME建模的最新进展
Annual reports in computational chemistry Pub Date : 2009-01-01 DOI: 10.1016/S1574-1400(09)00505-2
Junmei Wang, Tingjun Hou
{"title":"Chapter 5 Recent Advances on in silico ADME Modeling","authors":"Junmei Wang, Tingjun Hou","doi":"10.1016/S1574-1400(09)00505-2","DOIUrl":"https://doi.org/10.1016/S1574-1400(09)00505-2","url":null,"abstract":"","PeriodicalId":88823,"journal":{"name":"Annual reports in computational chemistry","volume":"5 1","pages":"101-127"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1574-1400(09)00505-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"56636000","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}
引用次数: 28
Chapter 6 Explicitly Correlated Coupled-Cluster Methods 第六章显式相关耦合簇方法
Annual reports in computational chemistry Pub Date : 2009-01-01 DOI: 10.1016/S1574-1400(09)00506-4
T. Shiozaki, Edward F. Valeev, S. Hirata
{"title":"Chapter 6 Explicitly Correlated Coupled-Cluster Methods","authors":"T. Shiozaki, Edward F. Valeev, S. Hirata","doi":"10.1016/S1574-1400(09)00506-4","DOIUrl":"https://doi.org/10.1016/S1574-1400(09)00506-4","url":null,"abstract":"","PeriodicalId":88823,"journal":{"name":"Annual reports in computational chemistry","volume":"85 1","pages":"131-148"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1574-1400(09)00506-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"56636013","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}
引用次数: 25
Methods for Monte Carlo simulations of biomacromolecules. 生物大分子的蒙特卡罗模拟方法。
Annual reports in computational chemistry Pub Date : 2009-01-01 DOI: 10.1016/S1574-1400(09)00503-9
Andreas Vitalis, Rohit V Pappu
{"title":"Methods for Monte Carlo simulations of biomacromolecules.","authors":"Andreas Vitalis,&nbsp;Rohit V Pappu","doi":"10.1016/S1574-1400(09)00503-9","DOIUrl":"10.1016/S1574-1400(09)00503-9","url":null,"abstract":"<p><p>The state-of-the-art for Monte Carlo (MC) simulations of biomacromolecules is reviewed. Available methodologies for sampling conformational equilibria and associations of biomacromolecules in the canonical ensemble, given a continuum description of the solvent environment, are reviewed. Detailed sections are provided dealing with the choice of degrees of freedom, the efficiencies of MC algorithms and algorithmic peculiarities, as well as the optimization of simple movesets. The issue of introducing correlations into elementary MC moves, and the applicability of such methods to simulations of biomacromolecules is discussed. A brief discussion of multicanonical methods and an overview of recent simulation work highlighting the potential of MC methods are also provided. It is argued that MC simulations, while underutilized biomacromolecular simulation community, hold promise for simulations of complex systems and phenomena that span multiple length scales, especially when used in conjunction with implicit solvation models or other coarse graining strategies.</p>","PeriodicalId":88823,"journal":{"name":"Annual reports in computational chemistry","volume":"5 ","pages":"49-76"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1574-1400(09)00503-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28953736","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}
引用次数: 103
Quantifying uncertainty and sampling quality in biomolecular simulations. 量化生物分子模拟中的不确定性和采样质量。
Annual reports in computational chemistry Pub Date : 2009-01-01 DOI: 10.1016/S1574-1400(09)00502-7
Alan Grossfield, Daniel M Zuckerman
{"title":"Quantifying uncertainty and sampling quality in biomolecular simulations.","authors":"Alan Grossfield, Daniel M Zuckerman","doi":"10.1016/S1574-1400(09)00502-7","DOIUrl":"10.1016/S1574-1400(09)00502-7","url":null,"abstract":"<p><p>Growing computing capacity and algorithmic advances have facilitated the study of increasingly large biomolecular systems at longer timescales. However, with these larger, more complex systems come questions about the quality of sampling and statistical convergence. What size systems can be sampled fully? If a system is not fully sampled, can certain \"fast variables\" be considered well-converged? How can one determine the statistical significance of observed results? The present review describes statistical tools and the underlying physical ideas necessary to address these questions. Basic definitions and ready-to-use analyses are provided, along with explicit recommendations. Such statistical analyses are of paramount importance in establishing the reliability of simulation data in any given study.</p>","PeriodicalId":88823,"journal":{"name":"Annual reports in computational chemistry","volume":"5 ","pages":"23-48"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2865156/pdf/nihms155855.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28975649","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}
引用次数: 0
Chapter 4 Accelerated Molecular Dynamics Methods: Introduction and Recent Developments 第四章加速分子动力学方法:介绍和最新进展
Annual reports in computational chemistry Pub Date : 2009-01-01 DOI: 10.1016/S1574-1400(09)00504-0
D. Perez, B. Uberuaga, Y. Shim, J. Amar, A. Voter
{"title":"Chapter 4 Accelerated Molecular Dynamics Methods: Introduction and Recent Developments","authors":"D. Perez, B. Uberuaga, Y. Shim, J. Amar, A. Voter","doi":"10.1016/S1574-1400(09)00504-0","DOIUrl":"https://doi.org/10.1016/S1574-1400(09)00504-0","url":null,"abstract":"","PeriodicalId":88823,"journal":{"name":"Annual reports in computational chemistry","volume":"5 1","pages":"79-98"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1574-1400(09)00504-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"56635992","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}
引用次数: 111
Chapter 1 – Structural Perspectives on Protein Evolution 第1章-蛋白质进化的结构观点
Annual reports in computational chemistry Pub Date : 2008-12-31 DOI: 10.1016/S1574-1400(08)00001-7
E. Franzosa, Yu Xia
{"title":"Chapter 1 – Structural Perspectives on Protein Evolution","authors":"E. Franzosa, Yu Xia","doi":"10.1016/S1574-1400(08)00001-7","DOIUrl":"https://doi.org/10.1016/S1574-1400(08)00001-7","url":null,"abstract":"","PeriodicalId":88823,"journal":{"name":"Annual reports in computational chemistry","volume":"4 1","pages":"3-21"},"PeriodicalIF":0.0,"publicationDate":"2008-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1574-1400(08)00001-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"56635265","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}
引用次数: 8
Stochastic Models for Polymerization Reactions Under Nonequilibrium Conditions 非平衡条件下聚合反应的随机模型
Annual reports in computational chemistry Pub Date : 2008-01-01 DOI: 10.1016/S1574-1400(08)00010-8
Yanping Qin, A. Popov, R. Hernandez
{"title":"Stochastic Models for Polymerization Reactions Under Nonequilibrium Conditions","authors":"Yanping Qin, A. Popov, R. Hernandez","doi":"10.1016/S1574-1400(08)00010-8","DOIUrl":"https://doi.org/10.1016/S1574-1400(08)00010-8","url":null,"abstract":"","PeriodicalId":88823,"journal":{"name":"Annual reports in computational chemistry","volume":"4 1","pages":"173-199"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1574-1400(08)00010-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"56635911","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}
引用次数: 2
Applications and Advances of QM/MM Methods in Computational Enzymology QM/MM方法在计算酶学中的应用与进展
Annual reports in computational chemistry Pub Date : 2008-01-01 DOI: 10.1016/S1574-1400(08)00009-1
A. Lodola, Christopher J. Woods, A. Mulholland
{"title":"Applications and Advances of QM/MM Methods in Computational Enzymology","authors":"A. Lodola, Christopher J. Woods, A. Mulholland","doi":"10.1016/S1574-1400(08)00009-1","DOIUrl":"https://doi.org/10.1016/S1574-1400(08)00009-1","url":null,"abstract":"","PeriodicalId":88823,"journal":{"name":"Annual reports in computational chemistry","volume":"4 1","pages":"155-169"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1574-1400(08)00009-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"56635905","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}
引用次数: 9
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