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Implementation and use of an atom-mapping procedure for similarity searching in databases of 3-D chemical structures 三维化学结构数据库中相似度搜索的原子映射程序的实现与使用
Tetrahedron Computer Methodology Pub Date : 1990-01-01 DOI: 10.1016/0898-5529(90)90160-A
Catherine A. Pepperrell , Robin Taylor , Peter Willett
{"title":"Implementation and use of an atom-mapping procedure for similarity searching in databases of 3-D chemical structures","authors":"Catherine A. Pepperrell ,&nbsp;Robin Taylor ,&nbsp;Peter Willett","doi":"10.1016/0898-5529(90)90160-A","DOIUrl":"10.1016/0898-5529(90)90160-A","url":null,"abstract":"<div><p>This paper discusses a procedure for calculating the degree of similarity between an input target molecule and each of the molecules in a database of 3-D chemical structures. A mapping algorithm is used to identify pairs of atoms, one from each of the molecules that are being compared, that lie at the centre of geometrically-related volumes of 3-D space. Techniques are described to increase the run-time efficiency of the basic procedure, so that it can be used for similarity searching in large 3-D databases, and to allow a wide range of types of inter-molecular similarity to be calculated.</p></div>","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 6","pages":"Pages 575-593"},"PeriodicalIF":0.0,"publicationDate":"1990-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/0898-5529(90)90160-A","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74399459","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
A very fast program for ESR spectrum simulation 一个非常快速的ESR频谱模拟程序
Tetrahedron Computer Methodology Pub Date : 1990-01-01 DOI: 10.1016/0898-5529(90)90112-L
Bruno Bienfait
{"title":"A very fast program for ESR spectrum simulation","authors":"Bruno Bienfait","doi":"10.1016/0898-5529(90)90112-L","DOIUrl":"10.1016/0898-5529(90)90112-L","url":null,"abstract":"<div><p>A fast ESR spectrum simulation program suitable for radicals in solution is described. The speed of the convolution algorithm is achieved by the use of integer arithmetic and precalculated lineshapes. FDC-ESR is written in C and runs on an IBM PC and ATARI ST (obtain program via TCM-Online) computers. A math coprocessor is not necessary.</p></div>","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 2","pages":"Pages 109-112"},"PeriodicalIF":0.0,"publicationDate":"1990-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/0898-5529(90)90112-L","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73983231","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
Heterocyclic reaction design with RDSS 用RDSS设计杂环反应
Tetrahedron Computer Methodology Pub Date : 1990-01-01 DOI: 10.1016/0898-5529(90)90070-O
F. Haase, K. Biedka ∗
{"title":"Heterocyclic reaction design with RDSS","authors":"F. Haase,&nbsp;K. Biedka ∗","doi":"10.1016/0898-5529(90)90070-O","DOIUrl":"10.1016/0898-5529(90)90070-O","url":null,"abstract":"<div><p>The paper gives a brief description of the synthesis planning program RDSS and deals with experience made in application to heterocyclic reactions. The main aim of the undertaken work was the test of the version RDSS V4.1 after completing a new synthon recognition program. A knowledge base consisting of some general synthesis rules and specialized heterocyclic mechanisms was built up to support this task. The results make sure that the knowledge based system RDSS may be a helpful tool for organic synthesis design.</p></div>","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 6","pages":"Pages 461-467"},"PeriodicalIF":0.0,"publicationDate":"1990-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/0898-5529(90)90070-O","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80722498","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
3D Database searching on the basis of ligand shape using the sperm prototype method 基于配体形状的精子原型法三维数据库检索
Tetrahedron Computer Methodology Pub Date : 1990-01-01 DOI: 10.1016/0898-5529(90)90161-Z
V.J. van Geerestein, N.C. Perry, P.D.J. Grootenhuis, C.A.G. Haasnoot
{"title":"3D Database searching on the basis of ligand shape using the sperm prototype method","authors":"V.J. van Geerestein,&nbsp;N.C. Perry,&nbsp;P.D.J. Grootenhuis,&nbsp;C.A.G. Haasnoot","doi":"10.1016/0898-5529(90)90161-Z","DOIUrl":"10.1016/0898-5529(90)90161-Z","url":null,"abstract":"<div><p>This paper describes a method for the rapid searching of <span>3d</span> structural databases for molecules showing <span>3d</span> shape similarity to a query structure. In the <span>sperm</span> program, molecular properties are projected onto the surface of a sphere and icosahedral symmetry is used to minimise storage requirements and accelerate comparison over all of <span>3d</span> rotational space. The results of searches of a 30,000 compound database for molecules with a <span>3d</span> shape resembling netropsin and daunomycin are described. In addition to molecules showing topological similarity to the query, hits are obtained showing considerable structural diversity. The results demonstrate that the method might be useful in the selection of new lead compounds as potential ligands for a given receptor.</p></div>","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 6","pages":"Pages 595-613"},"PeriodicalIF":0.0,"publicationDate":"1990-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/0898-5529(90)90161-Z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87791019","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: 35
General methodology and computer program for the exhaustive restoring of chemical structures by molecular connectivity indexes. Solution of the inverse problem in QSAR/QSPR 用分子连通性指数详尽恢复化学结构的一般方法和计算机程序。QSAR/QSPR中逆问题的求解
Tetrahedron Computer Methodology Pub Date : 1990-01-01 DOI: 10.1016/0898-5529(90)90066-H
Ekaterina V. Gordeeva, Marina S. Molchanova, Nikolai S. Zefirov ∗
{"title":"General methodology and computer program for the exhaustive restoring of chemical structures by molecular connectivity indexes. Solution of the inverse problem in QSAR/QSPR","authors":"Ekaterina V. Gordeeva,&nbsp;Marina S. Molchanova,&nbsp;Nikolai S. Zefirov ∗","doi":"10.1016/0898-5529(90)90066-H","DOIUrl":"10.1016/0898-5529(90)90066-H","url":null,"abstract":"<div><p>The first attempt to attack an intriguing inverse problem in QSAR/QSPR is presented. The special technique to the exhaustive targeted search of the structures with a given value of molecular connectivity index is described. The general methodology and the combinatorial algorithm are considered. The selection criteria for the correct generation of graphs and multigraphs with the given distribution of edge types or vertex types are developed. The RING program for the exhaustive generation of structures with the given connectivity index is described, and several examples of its successful application are discussed. A demo version of RING is included in this issue.</p></div>","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 6","pages":"Pages 389-415"},"PeriodicalIF":0.0,"publicationDate":"1990-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/0898-5529(90)90066-H","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88532042","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: 32
Comparative molecular field analysis (CoMFA). 2. Toward its use with 3D-structural databases 比较分子场分析(CoMFA)。2. 将其用于3d结构数据库
Tetrahedron Computer Methodology Pub Date : 1990-01-01 DOI: 10.1016/0898-5529(90)90120-W
Matthew Clark, Richard D. Cramer III ∗, Dumont M. Jones, David E. Patterson, Perry E. Simeroth
{"title":"Comparative molecular field analysis (CoMFA). 2. Toward its use with 3D-structural databases","authors":"Matthew Clark,&nbsp;Richard D. Cramer III ∗,&nbsp;Dumont M. Jones,&nbsp;David E. Patterson,&nbsp;Perry E. Simeroth","doi":"10.1016/0898-5529(90)90120-W","DOIUrl":"10.1016/0898-5529(90)90120-W","url":null,"abstract":"<div><p>The primary importance of molecular fields in biological recognition, attested by the number of reported successful CoMFA applications, suggests possible applications in 3D databases. In further support of this possibility, the probability of chance correlation using PLS in typical CoMFA applications is found to be about 5% or less for a cross-validated r<sup>2</sup> of 0.3 or greater, a “field fit” strategy for automating the alignment of molecules by seeking minimal differences in their fields is outlined, and a non-biological application of CoMFA, carbonyl hydration, is presented.</p></div>","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 1","pages":"Pages 47-59"},"PeriodicalIF":0.0,"publicationDate":"1990-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/0898-5529(90)90120-W","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88645532","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: 164
Conformationally restricted leukotriene antagonists. Modeling and assignment of structure of [(Octahydro-2-oxo-7-tetra-decylidene-2H-1-benzopyran-8-yl)thio]acetic acids 构象限制性白三烯拮抗剂。[(八氢-2-氧-7-四癸基- 2h -1-苯并吡喃-8-基)硫]乙酸的建模和结构赋值
Tetrahedron Computer Methodology Pub Date : 1990-01-01 DOI: 10.1016/0898-5529(90)90103-F
John Paolini ∗, Philip M. Weintraub ∗, Jeffrey S. Sabol, David A. Demeter, H.J.R. Weintraub
{"title":"Conformationally restricted leukotriene antagonists. Modeling and assignment of structure of [(Octahydro-2-oxo-7-tetra-decylidene-2H-1-benzopyran-8-yl)thio]acetic acids","authors":"John Paolini ∗,&nbsp;Philip M. Weintraub ∗,&nbsp;Jeffrey S. Sabol,&nbsp;David A. Demeter,&nbsp;H.J.R. Weintraub","doi":"10.1016/0898-5529(90)90103-F","DOIUrl":"10.1016/0898-5529(90)90103-F","url":null,"abstract":"<div><p>The proton NMR spectrum of the conformationally restricted, leukotriene antagonist [(octahydro-2-oxo-7-tetradecylidene-2H-1-benzopyran-8-yl)thio]acetic acid (<span><math><mtext>3a</mtext></math></span>) did not support a chair-chair conformation for the bicyclic ring system as is usually expected. Molecular mechanics and semi-empirical molecular orbital calculations, on the model compounds <span><math><mtext>3b</mtext></math></span> and <span><math><mtext>4b</mtext></math></span>, indicated that <span><math><mtext>3a</mtext></math></span> exists in a chair-boat rather than a chair-chair form. The findings of this computational study were confirmed by a subsequent x-ray analysis.</p></div>","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 5","pages":"Pages 271-276"},"PeriodicalIF":0.0,"publicationDate":"1990-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/0898-5529(90)90103-F","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77517303","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
Database structure and searching in MACCS-3D MACCS-3D数据库结构与检索
Tetrahedron Computer Methodology Pub Date : 1990-01-01 DOI: 10.1016/0898-5529(90)90164-4
Bradley D. Christie, Douglas R. Henry, W.Todd Wipke, Thomas E. Moock
{"title":"Database structure and searching in MACCS-3D","authors":"Bradley D. Christie,&nbsp;Douglas R. Henry,&nbsp;W.Todd Wipke,&nbsp;Thomas E. Moock","doi":"10.1016/0898-5529(90)90164-4","DOIUrl":"10.1016/0898-5529(90)90164-4","url":null,"abstract":"<div><p>The MACCS-3D program was developed to provide a three-dimensional (3D) structural database system for structure, substructure, geometric, and data searching purposes. Applications of the program include discovery of new drugs and agrochemicals to fit known or postulated pharmacophores, and identification of polymers and commercial chemicals whose physical and chemical properties depend on 3D structural features. This paper presents details of the data structures and algorithms used for 3D structural representation, storage, and searching in MACCS-3D. These include algorithms for exact match, substructure, geometric, submodel, and combined 3D structure-data searching. We also describe mechanisms used for 3D data storage and geometric search keys. Integration of MACCS-3D with new chemical representation and search capabilities of the MACCS-II system are briefly described. Finally, new developments in MACCS-3D are described, in light of current and future trends in 3D searching.</p></div>","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 6","pages":"Pages 653-664"},"PeriodicalIF":0.0,"publicationDate":"1990-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/0898-5529(90)90164-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77299743","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: 17
An alternative view of reaction similarity: Citation analysis 反应相似度的另一种观点:引文分析
Tetrahedron Computer Methodology Pub Date : 1990-01-01 DOI: 10.1016/0898-5529(90)90111-K
W.Todd Wipke ∗ , George Vladutz
{"title":"An alternative view of reaction similarity: Citation analysis","authors":"W.Todd Wipke ∗ ,&nbsp;George Vladutz","doi":"10.1016/0898-5529(90)90111-K","DOIUrl":"10.1016/0898-5529(90)90111-K","url":null,"abstract":"<div><p>Previous work on reaction similarity was based on co-occurence of structural and reaction center keys between reactions in computer-readable databases of reactions. This work demonstrates that similar reactions can be found, even though they are not computer-readable, through citation analysis. Complete citation search results are included on disk.</p></div>","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 2","pages":"Pages 83-107"},"PeriodicalIF":0.0,"publicationDate":"1990-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/0898-5529(90)90111-K","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77317059","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: 5
Experiences building and searching the Chapman & Hall Dictionary of Drugs 建立和搜索查普曼和霍尔药物词典的经验
Tetrahedron Computer Methodology Pub Date : 1990-01-01 DOI: 10.1016/0898-5529(90)90165-5
Keith Davies, Roger Upton
{"title":"Experiences building and searching the Chapman & Hall Dictionary of Drugs","authors":"Keith Davies,&nbsp;Roger Upton","doi":"10.1016/0898-5529(90)90165-5","DOIUrl":"10.1016/0898-5529(90)90165-5","url":null,"abstract":"<div><p>The Chapman and Hall <em>Dictionary of Drugs</em> is a source of information on over 6000 drugs and their derivatives. The printed form includes much physical and pharmacological data abstracted from patents as well as 2D drawings. The 2D connection tables were made available to Chemical Design and 3D structures were generated and stored in a ChemDBS-3D database. From the initial stored structure, the 3D conformational distance keys were generated in a second step. The computer resources used are presented and these indicate that scaling the automated build/keying procedures to include several 100,000s of compounds is a practical proposition. Some search examples are used to illustrate the screening effects of 3D key searches and the relative importance of using conformational flexibility in finding new hits.</p></div>","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 6","pages":"Pages 665-671"},"PeriodicalIF":0.0,"publicationDate":"1990-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/0898-5529(90)90165-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86574672","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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