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TRAJAN: A tool with which analyze trajectories from molecular simulations 图拉真:一种分析分子模拟轨迹的工具
Journal of molecular graphics Pub Date : 1996-06-01 DOI: 10.1016/0263-7855(96)89172-7
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引用次数: 0
The inhibition of α-chymotrypsin predicted using theoretically derived molecular properties α-凝乳胰蛋白酶的抑制作用用理论推导的分子性质预测
Journal of molecular graphics Pub Date : 1996-06-01 DOI: 10.1016/0263-7855(96)89169-7
{"title":"The inhibition of α-chymotrypsin predicted using theoretically derived molecular properties","authors":"","doi":"10.1016/0263-7855(96)89169-7","DOIUrl":"https://doi.org/10.1016/0263-7855(96)89169-7","url":null,"abstract":"","PeriodicalId":73837,"journal":{"name":"Journal of molecular graphics","volume":"14 3","pages":"Page 142"},"PeriodicalIF":0.0,"publicationDate":"1996-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/0263-7855(96)89169-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"137317220","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
Interaction of human leukocyte elastase with a N-aryl azetidinone suicide sustate: Conformational analyses based on the mechanism of action of serine proteinases 人白细胞弹性酶与n -芳基氮杂二酮自杀维持体的相互作用:基于丝氨酸蛋白酶作用机制的构象分析
Journal of molecular graphics Pub Date : 1996-06-01 DOI: 10.1016/0263-7855(96)89171-5
{"title":"Interaction of human leukocyte elastase with a N-aryl azetidinone suicide sustate: Conformational analyses based on the mechanism of action of serine proteinases","authors":"","doi":"10.1016/0263-7855(96)89171-5","DOIUrl":"https://doi.org/10.1016/0263-7855(96)89171-5","url":null,"abstract":"","PeriodicalId":73837,"journal":{"name":"Journal of molecular graphics","volume":"14 3","pages":"Page 145"},"PeriodicalIF":0.0,"publicationDate":"1996-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/0263-7855(96)89171-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"137317222","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
DL_POLY_2.0: A general-purpose parallel molecular dynamics simulation package DL_POLY_2.0:一个通用的并行分子动力学模拟包
Journal of molecular graphics Pub Date : 1996-06-01 DOI: 10.1016/S0263-7855(96)00043-4
W. Smith, T.R. Forester
{"title":"DL_POLY_2.0: A general-purpose parallel molecular dynamics simulation package","authors":"W. Smith,&nbsp;T.R. Forester","doi":"10.1016/S0263-7855(96)00043-4","DOIUrl":"10.1016/S0263-7855(96)00043-4","url":null,"abstract":"<div><p>DL_POLY_2.0 is a general-purpose parallel molecular dynamics simulation package developed at Daresbury Laboratory under the auspices of the Council for the Central Laboratory of the Research Councils. Written to support academic research, it has a wide range of applications and is designed to run on a wide range of computers: from single processor workstations to parallel supercomputers. Its structure, functionality, performance, and availability are described.</p></div>","PeriodicalId":73837,"journal":{"name":"Journal of molecular graphics","volume":"14 3","pages":"Pages 136-141"},"PeriodicalIF":0.0,"publicationDate":"1996-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0263-7855(96)00043-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"19866665","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: 1778
Sequential and parallel molecular mechanics calculations 顺序和平行分子力学计算
Journal of molecular graphics Pub Date : 1996-06-01 DOI: 10.1016/S0263-7855(96)00042-2
Davis N.J. White
{"title":"Sequential and parallel molecular mechanics calculations","authors":"Davis N.J. White","doi":"10.1016/S0263-7855(96)00042-2","DOIUrl":"10.1016/S0263-7855(96)00042-2","url":null,"abstract":"<div><p>This article describes a gradient algorithm for the computational optimization of model molecular structures, and discusses the various compromises inherent in the practical expression of the algorithm in a Fortran computer program (VULCAN) for both sequential and parallel computers. Details are given of some previously undiscussed properties of gradient algorithms; various acceleration techniques are compared: and some traps for the unwary are highlighted.</p></div>","PeriodicalId":73837,"journal":{"name":"Journal of molecular graphics","volume":"14 3","pages":"Pages 119-129"},"PeriodicalIF":0.0,"publicationDate":"1996-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0263-7855(96)00042-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"19866663","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 model of interleukin 12 that highlights amino acid sequence homologies with adhesion domains and gastrointestinal peptides 白细胞介素12的分子模型，强调与粘附结构域和胃肠道肽的氨基酸序列同源性
Journal of molecular graphics Pub Date : 1996-06-01 DOI: 10.1016/S0263-7855(96)00044-6
Donard S. Dwyer
{"title":"Molecular model of interleukin 12 that highlights amino acid sequence homologies with adhesion domains and gastrointestinal peptides","authors":"Donard S. Dwyer","doi":"10.1016/S0263-7855(96)00044-6","DOIUrl":"10.1016/S0263-7855(96)00044-6","url":null,"abstract":"<div><p>A three-dimensional (3-D) model of both subunits of interleukin 12 (IL-12) has been created through molecular modeling. Initial assignment of coordinates in the model of the p40 subunit was based on established amino acid sequence homology between the second and third domains of p40 and the human growth hormone receptor (GHR) and new observations of similarity between the first domain of p40 and the N-terminal domain of CD4. Human growth hormone (GH) served as the reference protein for the p35 chain. Furthermore, thorough analysis of the amino acid sequence of IL-12 revealed two distinct regions of the p40 subunit that display homology with other proteins. The first region (in domain two) contains the sequence RGD, which is found in adhesion proteins (such as fibronectin), and the nearby sequence VTCG, which occurs in a diverse set of molecules, including thrombospondin, properdin, and circumsporozoite proteins of <em>Plasmodium</em>. The second region of homology spans the third domain of p40 and shows marked similarity with the gastrointestinal peptides, such as secretin and glucagon and their preprohormones. We conclude (1) that the regions of homology define functionally important segments of p40 that are fully exposed at the protein surface, and (2) that the third domain of p40 (and its equivalent in the cytokine receptor family) is derived from the same ancestral genes as the gastrointestinal peptides.</p></div>","PeriodicalId":73837,"journal":{"name":"Journal of molecular graphics","volume":"14 3","pages":"Pages 148-157"},"PeriodicalIF":0.0,"publicationDate":"1996-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0263-7855(96)00044-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"19866666","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: 11
TRAJAN: A tool for analyzing trajectories from molecular simulations 图拉真:一个分析分子模拟轨迹的工具
Journal of molecular graphics Pub Date : 1996-06-01 DOI: 10.1016/S0263-7855(96)00059-8
Graham A. Worth , Christophe Lecuyer, Rebecca C. Wade ∗
{"title":"TRAJAN: A tool for analyzing trajectories from molecular simulations","authors":"Graham A. Worth ,&nbsp;Christophe Lecuyer,&nbsp;Rebecca C. Wade ∗","doi":"10.1016/S0263-7855(96)00059-8","DOIUrl":"10.1016/S0263-7855(96)00059-8","url":null,"abstract":"<div><p>Molecular dynamics simulations of biological systems are notoriously difficult to analyze because of the complexity of the information that they contain. We describe a new method for analyzing trajectories from simulations in order to extract important features of the motion. The trajectory of each atom is partitioned into conformation wells, in each of which its motion is assumed to be predominantly harmonic oscillation around an average position. Thus each atom moves anharmonically through a sequence of wells during the trajectory. The movement of atoms between wells, their ellipsoids of motion within each well, and correlations in the motion of atoms are quantified and can be visualized with molecular graphics. The TRAJAN analysis procedure is applicable to trajectories from equilibrium and nonequilibrium simulations and is not restricted to molecular dynamics simulations. Its application is demonstrated for a range of model systems.</p></div>","PeriodicalId":73837,"journal":{"name":"Journal of molecular graphics","volume":"14 3","pages":"Pages 173-182"},"PeriodicalIF":0.0,"publicationDate":"1996-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0263-7855(96)00059-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"19866669","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
A compendium of potential energy maps of zeolites and molecular sieves 沸石和分子筛的势能图简编
Journal of molecular graphics Pub Date : 1996-04-01 DOI: 10.1016/0263-7855(96)00040-9
D. Keffer , Vishwas Gupta , David Kim , Elizabeth Lenz , H. Ted Davis , Alon V. McCormick
{"title":"A compendium of potential energy maps of zeolites and molecular sieves","authors":"D. Keffer ,&nbsp;Vishwas Gupta ,&nbsp;David Kim ,&nbsp;Elizabeth Lenz ,&nbsp;H. Ted Davis ,&nbsp;Alon V. McCormick","doi":"10.1016/0263-7855(96)00040-9","DOIUrl":"10.1016/0263-7855(96)00040-9","url":null,"abstract":"<div><p>We present potential maps of xenon in 20 different zeolites and molecular sieves. The potential maps reveal both the accessible pore volume and localized adsorption sites and so are important in understanding adsorption and diffusion processes in nanoporous materials. We examine zeolites and molecular sieves with one-dimensional channel-like nanopores (zeolite-Theta 1, AlPO<sub>4</sub>-5, zeolite-Omega, zeolite-L, ZSM-12, AlPO<sub>4</sub>-8, and VPI-5), with two-dimensional intersecting channel-like nanopores (ZSM-5 [silicalite], ZSM-11, ferrierite, mordenite, and zeolite-Beta), and with three-dimensionally connected cagelike nanopores (zeolite-A, zeolite-Rho, zeolite-Y, sodalite, chabazite, cloverite, cation-poor zeolite-A, and cation-rich zeolite-A). We report the fraction of pore volume accessible, the maximum energy well depth at the adsorption sites, and the activation energy to move between sites. We note several examples of surprising similarities and differences between various molecular sieves. In several instances, we show that these potential profiles are relevant for other small Lennard-Jones-like molecules. By comparison with published Monte Carlo and molecular dynamics simulations, we show that the density distributions of adsorbates at low density are well predicted by the potential maps.</p></div>","PeriodicalId":73837,"journal":{"name":"Journal of molecular graphics","volume":"14 2","pages":"Pages 108-116"},"PeriodicalIF":0.0,"publicationDate":"1996-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/0263-7855(96)00040-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"19804577","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: 26
Stages in the construction of stereograms of molecular models 构建分子模型立体图的阶段
Journal of molecular graphics Pub Date : 1996-04-01 DOI: 10.1016/0263-7855(96)00029-X
Nikodem Miranowicz, Andrzej Burewicz
{"title":"Stages in the construction of stereograms of molecular models","authors":"Nikodem Miranowicz,&nbsp;Andrzej Burewicz","doi":"10.1016/0263-7855(96)00029-X","DOIUrl":"10.1016/0263-7855(96)00029-X","url":null,"abstract":"<div><p>In this article an analysis is performed of the results of stereogram construction using computer programs that model chemical compounds. Considerations about how best to represent models of molecules and improve legibility of stereograms are presented. An original diagrammatic substitute for the picture of a sphere, suitable for application in stereoscopic models of molecules, is proposed.</p></div>","PeriodicalId":73837,"journal":{"name":"Journal of molecular graphics","volume":"14 2","pages":"Pages 73-77"},"PeriodicalIF":0.0,"publicationDate":"1996-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/0263-7855(96)00029-X","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"19802914","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
Reviews in computational chemistry, vol. 7 计算化学评论，第7卷
Journal of molecular graphics Pub Date : 1996-04-01 DOI: 10.1016/0263-7855(96)00031-8
Ruth Pachter
{"title":"Reviews in computational chemistry, vol. 7","authors":"Ruth Pachter","doi":"10.1016/0263-7855(96)00031-8","DOIUrl":"10.1016/0263-7855(96)00031-8","url":null,"abstract":"","PeriodicalId":73837,"journal":{"name":"Journal of molecular graphics","volume":"14 2","pages":"Page 117"},"PeriodicalIF":0.0,"publicationDate":"1996-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/0263-7855(96)00031-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"53794871","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: 6
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