{"title":"Analytically defined surfaces to analyze molecular interaction properties","authors":"R.R. Gabdoulline, R.C. Wade","doi":"10.1016/S0263-7855(97)00008-8","DOIUrl":"10.1016/S0263-7855(97)00008-8","url":null,"abstract":"<div><p>Molecular surfaces are widely used for characterizing molecules and displaying and quantifying their interaction properties. Here we consider molecular surfaces defined as isocontours of a function (a sum of exponential functions centered on each atom) that approximately represents electron density. The smoothness is advantageous for surface mapping of molecular properties (e.g., electrostatic potential). By varying parameters, these surfaces can be constructed to represent the van der Waals or solvent-accessible surface of a molecular with any accuracy. We describe numerical algorithms to operate on the analytically defined surfaces. Two applications are considered: (1) We define and locate extremal points of molecular properties on the surfaces. The extremal points provide a compact representation of a property on a surface, obviating the necessity to compute values of the property on an array of surface points as is usually done; (2) a molecular surface patch or interface is projected onto a flat surface (by introducing curvilinear coordinates) with approximate conservation of area for analysis purposes. Applications to studies of protein-protein interactions are described.</p></div>","PeriodicalId":73837,"journal":{"name":"Journal of molecular graphics","volume":"14 6","pages":"Pages 341-353"},"PeriodicalIF":0.0,"publicationDate":"1996-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0263-7855(97)00008-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20141675","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":"Chem-X/INVENTORY now available","authors":"","doi":"10.1016/S0263-7855(96)90042-9","DOIUrl":"https://doi.org/10.1016/S0263-7855(96)90042-9","url":null,"abstract":"","PeriodicalId":73837,"journal":{"name":"Journal of molecular graphics","volume":"14 6","pages":"Pages 385-386"},"PeriodicalIF":0.0,"publicationDate":"1996-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0263-7855(96)90042-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91597033","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":"A theoretical study of CC bond formation in the methanol to gasoline process: The role of water","authors":"","doi":"10.1016/S0263-7855(97)89621-X","DOIUrl":"https://doi.org/10.1016/S0263-7855(97)89621-X","url":null,"abstract":"","PeriodicalId":73837,"journal":{"name":"Journal of molecular graphics","volume":"14 6","pages":"Page 378"},"PeriodicalIF":0.0,"publicationDate":"1996-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0263-7855(97)89621-X","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91685853","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":"Molecular mechanics study of organometallic complexes in crystalline silica matrices using the ESFF forcefield","authors":"","doi":"10.1016/S0263-7855(97)89630-0","DOIUrl":"https://doi.org/10.1016/S0263-7855(97)89630-0","url":null,"abstract":"","PeriodicalId":73837,"journal":{"name":"Journal of molecular graphics","volume":"14 6","pages":"Page 381"},"PeriodicalIF":0.0,"publicationDate":"1996-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0263-7855(97)89630-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89988677","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":"Structure and properties of cycloolefinic polymers: Simulation and experiment","authors":"","doi":"10.1016/S0263-7855(97)89626-9","DOIUrl":"https://doi.org/10.1016/S0263-7855(97)89626-9","url":null,"abstract":"","PeriodicalId":73837,"journal":{"name":"Journal of molecular graphics","volume":"14 6","pages":"Page 380"},"PeriodicalIF":0.0,"publicationDate":"1996-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0263-7855(97)89626-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89989173","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":"Synopsys and informix form strategic partnership","authors":"","doi":"10.1016/S0263-7855(96)90036-3","DOIUrl":"https://doi.org/10.1016/S0263-7855(96)90036-3","url":null,"abstract":"","PeriodicalId":73837,"journal":{"name":"Journal of molecular graphics","volume":"14 6","pages":"Pages 383-384"},"PeriodicalIF":0.0,"publicationDate":"1996-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0263-7855(96)90036-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89989176","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":"MDMovie: A molecular dynamics viewing tool","authors":"Jerry P. Greenberg","doi":"10.1016/S0263-7855(96)00079-3","DOIUrl":"10.1016/S0263-7855(96)00079-3","url":null,"abstract":"<div><p>The graphics program MDMovie (Molecular Dynamics Movie), written in C using IRIS GL graphics library calls, is designed to facilitate the visualization and interpretation of empirical force field data. MDMovie was created and initially adapted in accord with the needs of physical chemists and thereafter became an expandable analysis tool. Capabilities include the display of chemical structure, animation of molecular dynamics and Monte Carlo trajectories, and the visual representation of various vector and scalar dynamical properties. In addition to being a research tool, MDMovie has features for creating presentation videos and hardcopy output. A library is also available for linking to Fortran simulation codes running on a remote machine and connecting to MDMovie via a socket connection. MDMovie continues to be an ongoing research project and new features are actively being added in collaboration with various research groups. Future plans include porting to OpenGL and the design of an X11-based user interface.</p></div>","PeriodicalId":73837,"journal":{"name":"Journal of molecular graphics","volume":"14 5","pages":"Pages 287-290"},"PeriodicalIF":0.0,"publicationDate":"1996-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0263-7855(96)00079-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20047259","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":"A molecular model of the carbohydrate recognition domain of a rat macrophage lectin and analysis of its binding site","authors":"Jürgen Bajorath","doi":"10.1016/S0263-7855(96)00075-6","DOIUrl":"10.1016/S0263-7855(96)00075-6","url":null,"abstract":"<div><p>A three-dimensional model of the carbohydrate recognition domain of a rat macrophage C-type lectin has been constructed by comparative modeling and assessed by inverse folding analysis. Comparative modeling in the presence of low sequence similarity was based on information provided by comparison of X-ray structures and sequence-structure alignments. The sequence-structure compatibility of the model was sound. Its binding site was analyzed in comparison to the X-ray structure of a galactose-specific mutant of the mannose-binding protein. The specificity of the macrophage lectin was discussed in light of mutagenesis data on asialoglycoprotein receptors.</p></div>","PeriodicalId":73837,"journal":{"name":"Journal of molecular graphics","volume":"14 5","pages":"Pages 297-301"},"PeriodicalIF":0.0,"publicationDate":"1996-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0263-7855(96)00075-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20047261","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}