Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding最新文献

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E-optimal solutions to distance geometry problems via global continuation 基于全局延拓的距离几何问题的e -最优解
J. J. Moré, Zhi-jun Wu
{"title":"E-optimal solutions to distance geometry problems via global continuation","authors":"J. J. Moré, Zhi-jun Wu","doi":"10.1090/dimacs/023/10","DOIUrl":"https://doi.org/10.1090/dimacs/023/10","url":null,"abstract":"","PeriodicalId":347710,"journal":{"name":"Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding","volume":"78 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1995-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121866805","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: 41
Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, Proceedings of a DIMACS Workshop, USA, March 20-21, 1995 非凸能量函数的全局最小化:分子构象和蛋白质折叠,美国DIMACS研讨会论文集,1995年3月20-21日
P. Pardalos, D. Shalloway, G. Xue
{"title":"Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, Proceedings of a DIMACS Workshop, USA, March 20-21, 1995","authors":"P. Pardalos, D. Shalloway, G. Xue","doi":"10.1090/DIMACS/023","DOIUrl":"https://doi.org/10.1090/DIMACS/023","url":null,"abstract":"","PeriodicalId":347710,"journal":{"name":"Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding","volume":"78 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1995-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129364767","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: 71
Global optimization methods for protein folding problems 蛋白质折叠问题的全局优化方法
R. Byrd, E. Eskow, A. Hoek, Bobby Schnabel, Chung-Shang Shao, Zhihong Zou
{"title":"Global optimization methods for protein folding problems","authors":"R. Byrd, E. Eskow, A. Hoek, Bobby Schnabel, Chung-Shang Shao, Zhihong Zou","doi":"10.1090/dimacs/023/03","DOIUrl":"https://doi.org/10.1090/dimacs/023/03","url":null,"abstract":"The problem of nding the naturally occurring structure of a pro tein is believed to correspond to minimizing the free or potential energy of the protein This is generally a very di cult global optimizationproblem with a large number of parameters and a huge number of local minimizers includ ing many with function values near that of the global minimizer This paper presents a new global optimization method for such problems The method consists of an initial phase that locates some reasonably low local minimizers of the energy function followed by the main phase that progresses from the best current local minimizers to even lower local minimizers The method combines portions that work on small subsets of the parameters including small scale global optimizations using stochastic methods with local minimizations in volving all the parameters In computational tests on the protein polyalanine with up to amino acids internal parameters the method appears to be very successful in nding the lowest energy structures The largest case is particularly signi cant because the lowest energy structures that are found include ones that exhibit interesting tertiary as opposed to just secondary","PeriodicalId":347710,"journal":{"name":"Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding","volume":"31 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122146053","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: 20
A minimal principle in the phase problem of X-ray crystallography x射线晶体学中相位问题的最小原理
H. Hauptman
{"title":"A minimal principle in the phase problem of X-ray crystallography","authors":"H. Hauptman","doi":"10.1090/dimacs/023/06","DOIUrl":"https://doi.org/10.1090/dimacs/023/06","url":null,"abstract":"","PeriodicalId":347710,"journal":{"name":"Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122730920","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
Thermodynamics and kinetics of protein folding 蛋白质折叠的热力学和动力学
A. Sali, E. Shakhnovich, M. Karplus
{"title":"Thermodynamics and kinetics of protein folding","authors":"A. Sali, E. Shakhnovich, M. Karplus","doi":"10.1090/dimacs/023/13","DOIUrl":"https://doi.org/10.1090/dimacs/023/13","url":null,"abstract":"","PeriodicalId":347710,"journal":{"name":"Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding","volume":"83 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114624922","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: 10
Global minimization on rugged energy landscapes 在崎岖的能源景观上实现全局最小化
P. Amara, Jianpeng Ma, J. Straub
{"title":"Global minimization on rugged energy landscapes","authors":"P. Amara, Jianpeng Ma, J. Straub","doi":"10.1090/dimacs/023/01","DOIUrl":"https://doi.org/10.1090/dimacs/023/01","url":null,"abstract":"","PeriodicalId":347710,"journal":{"name":"Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding","volume":"5 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130390343","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
Molecular structure determination by convex, global underestimation of local energy minima 通过局部能量最小值的凸、全局低估来确定分子结构
A. Phillips, J. B. Rosen, V. H. Walke
{"title":"Molecular structure determination by convex, global underestimation of local energy minima","authors":"A. Phillips, J. B. Rosen, V. H. Walke","doi":"10.1090/dimacs/023/12","DOIUrl":"https://doi.org/10.1090/dimacs/023/12","url":null,"abstract":"The determination of a stable molecular structure can often be formulated in terms of calculating the global (or approximate global) minimum of a potential energy function. Computing the global minimum of this function is very difficult because it typically has a very large number of local minima which may grow exponentially with molecule size. The optimization method presented involves collecting a large number of conformers, each attained by finding a local minimum of the potential energy function from a random starting point. The information from these conformers is then used to form a convex quadratic global underestimating function for the potential energy of all known conformers. This underestimator is an L 1 approximation to all known local minima, and is obtained by a linear programming formulation and solution. The minimum of this underestimator is used to predict the global minimum for the function, allowing a localized conformer search to be performed based on the predicted minimum. The new set of conformers generated by the localized search serves as the basis for another quadratic underestimation step in an iterative algorithm. This algorithm has been used to determine the structures of homopolymers of lengthn ≤ 30 with no sidechains. While it is estimated that there areO(3n) local minima for a chain of length n, this method requires O(n4) computing time on average. It is also shown that the global minimum potential energy values lie on a concave quadratic curve for n ≤ 30. This important property permits estimation of the minimum energy for larger molecules, and also can be used to accelerate the global minimization algorithm.","PeriodicalId":347710,"journal":{"name":"Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding","volume":"10 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114187147","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: 30
The design of chromophore containing biomolecules 含生物分子的发色团的设计
R. Pachter, Zhiqiang Wang, J. A. Lupo, S. Fairchild, Brian Sennett
{"title":"The design of chromophore containing biomolecules","authors":"R. Pachter, Zhiqiang Wang, J. A. Lupo, S. Fairchild, Brian Sennett","doi":"10.1090/dimacs/023/11","DOIUrl":"https://doi.org/10.1090/dimacs/023/11","url":null,"abstract":"","PeriodicalId":347710,"journal":{"name":"Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding","volume":"16 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126395037","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: 0
Energy directed conformational search of protein loops and segments 蛋白质环和片段的能量定向构象搜索
R. Bruccoleri
{"title":"Energy directed conformational search of protein loops and segments","authors":"R. Bruccoleri","doi":"10.1090/dimacs/023/02","DOIUrl":"https://doi.org/10.1090/dimacs/023/02","url":null,"abstract":"","PeriodicalId":347710,"journal":{"name":"Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding","volume":"5 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125613160","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: 0
Tracking metastable states to free-energy global minima 追踪亚稳态到自由能全球最小值
B. Church, M. Orešič, D. Shalloway
{"title":"Tracking metastable states to free-energy global minima","authors":"B. Church, M. Orešič, D. Shalloway","doi":"10.1090/dimacs/023/04","DOIUrl":"https://doi.org/10.1090/dimacs/023/04","url":null,"abstract":"","PeriodicalId":347710,"journal":{"name":"Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding","volume":"22 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132314115","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: 10
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