Tetrahedron Computer Methodology最新文献

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The golden age of computational chemistry 计算化学的黄金时代
Tetrahedron Computer Methodology Pub Date : 1990-01-01 DOI: 10.1016/0898-5529(90)90064-F
W.Todd Wipke (Editor-in-Chief)
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引用次数: 0
Neural network analysis of protein tertiary structure 蛋白质三级结构的神经网络分析
Tetrahedron Computer Methodology Pub Date : 1990-01-01 DOI: 10.1016/0898-5529(90)90052-A
George L. Wilcox , Marius Poliac , Michael N. Liebman
{"title":"Neural network analysis of protein tertiary structure","authors":"George L. Wilcox ,&nbsp;Marius Poliac ,&nbsp;Michael N. Liebman","doi":"10.1016/0898-5529(90)90052-A","DOIUrl":"10.1016/0898-5529(90)90052-A","url":null,"abstract":"<div><p>We describe a large scale application of a back-propagation neural network to the analysis, classification and prediction of protein secondary and tertiary structure from sequence information alone. A back-propagation network called BigNet has been implemented along with a Network Description Language (NDL) on the 512 MWord Cray 2 at the Minnesota Supercomputer Center. The proof-of-concept experiments described here used a small, heterologous training set of small protein structures (15 proteins each with less than 133 residues) from the Brookhaven Protein Data Bank (PDB). Simulations with one hidden layer and one half to ten million connections execute at three to five million connection updates per second in full back-propagation learning mode and routinely converge to solutions where input of hydrophobicity-coded sequence yields output distance matrices with 0.3 to 1.5% RMS deviation from actual distance matrices. Although the training set used is too small to expect useful generalization, some evidence of generalization was evident in similarity of learning progress of homologous pairs within the training set and in production of novel distance matrix outputs upon presentation with novel input sequences. The discussion addresses limitations in the current implementation, plans for software improvements, and characteristics of future training sets.</p></div>","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 3","pages":"Pages 191-204, IN4, 205-211"},"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)90052-A","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87743259","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
Neural network applications in synthetic organic chemistry: I. A hybrid system which performs retrosynthetic analysis 神经网络在合成有机化学中的应用:1 .进行反合成分析的混合系统
Tetrahedron Computer Methodology Pub Date : 1990-01-01 DOI: 10.1016/0898-5529(90)90049-E
Hudson H. Luce, Rakesh Govind
{"title":"Neural network applications in synthetic organic chemistry: I. A hybrid system which performs retrosynthetic analysis","authors":"Hudson H. Luce,&nbsp;Rakesh Govind","doi":"10.1016/0898-5529(90)90049-E","DOIUrl":"https://doi.org/10.1016/0898-5529(90)90049-E","url":null,"abstract":"<div><p>Organic chemists, when creating and planning the synthesis of new molecules, use a cognitive process known as “retrosynthetic analysis”, along with an ordered set of interrelations between various chemical elements, compounds, and properties embodied in what is termed as “chemical intuition”. Retrosynthetic analysis can be represented as a pattern recognition problem, and as such, can be modelled using neural networks, in which ordered representations (which model “chemical intuition”) of molecular subunits and features are used as input. Actual results from one neural network which performs tactical disconnections α and β to carbonyl groups are presented and discussed, as well as the structure for the hybrid expert system, incorporating a collection of neural nets. The program is included, along with all files needed to run ACME.</p></div>","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 3","pages":"Pages 143-161"},"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)90049-E","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138198909","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
Characteristics of computer-generated 3D and related molecular property data for CAS registry substances 计算机生成的CAS登记物质三维特征及相关分子特性数据
Tetrahedron Computer Methodology Pub Date : 1990-01-01 DOI: 10.1016/0898-5529(90)90163-3
William Fisanick, Kevin P. Cross, Andrew Rusinko III
{"title":"Characteristics of computer-generated 3D and related molecular property data for CAS registry substances","authors":"William Fisanick,&nbsp;Kevin P. Cross,&nbsp;Andrew Rusinko III","doi":"10.1016/0898-5529(90)90163-3","DOIUrl":"10.1016/0898-5529(90)90163-3","url":null,"abstract":"<div><p>Chemical Abstracts Service (CAS) is exploring approaches for searching on 3D and related molecular property data for CAS Registry substances. This searching includes “fuzzy-match” similarity searching. As the first part of this effort, the 3D coordinates have been generated by the CONCORD program for sample files of Registry substances, including a file of ring system, “framework” substances. In addition, molecular property data such as partial atom charges and ionization potentials have been derived from the corresponding 2D and/or 3D data via computational chemistry programs. Experimental software is being developed to identify, analyze and search various characteristics of 3D and molecular property data. These characteristics include 3D structural, flexibility, shape and molecular property features for portions of a substance and/or the entire substance. This paper will discuss some preliminary results of the analysis and searching of these data characteristics.</p></div>","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 6","pages":"Pages 635-652"},"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)90163-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74296633","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: 14
Automatic generation of 3D-atomic coordinates for organic molecules 自动生成三维原子坐标的有机分子
Tetrahedron Computer Methodology Pub Date : 1990-01-01 DOI: 10.1016/0898-5529(90)90156-3
J. Gasteiger, C. Rudolph, J. Sadowski
{"title":"Automatic generation of 3D-atomic coordinates for organic molecules","authors":"J. Gasteiger,&nbsp;C. Rudolph,&nbsp;J. Sadowski","doi":"10.1016/0898-5529(90)90156-3","DOIUrl":"10.1016/0898-5529(90)90156-3","url":null,"abstract":"<div><p>A system has been developed that can automatically generate three-dimensional atomic coordinates from the constitution of a molecule as expressed by a connection table. The program, CORINA, is applicable to the entire range of organic chemistry. It can also handle structures that are beyond the scope of some other programs, <span><math><mtext>e.g.</mtext></math></span>, macrocyclic and polymacrocyclic molecules. Computation times are short and the results compare favorably with data from X-ray crystallography and with those of molecular mechanics calculations.</p></div>","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 6","pages":"Pages 537-547"},"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)90156-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74018272","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: 462
Aromaticity as a quantitative concept part V: A comparison of semi-empirical methods for the calculation of molecular geometries of heteroaromatic compounds and application of the AM1 and MNDO methods to the calculation of Bird's aromaticity indices 芳香性作为定量概念第五部分:计算杂芳香化合物分子几何形状的半经验方法的比较,以及AM1和MNDO方法在Bird’s芳香性指数计算中的应用
Tetrahedron Computer Methodology Pub Date : 1990-01-01 DOI: 10.1016/0898-5529(90)90102-E
Alan R. Katritzky ∗ , Miroslaw Szafran , Ernst Anders , N. Malhotra, Sana Ullah Chaudry
{"title":"Aromaticity as a quantitative concept part V: A comparison of semi-empirical methods for the calculation of molecular geometries of heteroaromatic compounds and application of the AM1 and MNDO methods to the calculation of Bird's aromaticity indices","authors":"Alan R. Katritzky ∗ ,&nbsp;Miroslaw Szafran ,&nbsp;Ernst Anders ,&nbsp;N. Malhotra,&nbsp;Sana Ullah Chaudry","doi":"10.1016/0898-5529(90)90102-E","DOIUrl":"10.1016/0898-5529(90)90102-E","url":null,"abstract":"<div><p>The MINDO/3, MNDO, and AM1 geometries for five and six membered heteroaromatics have been compared with available experimental data and with some ab initio geometries. Geometry optimizations using the AM1 and MNDO methods gave the best results of the semi-empirical methods examined and yielded molecular geometries in good agreement with available experimental bond angles of all types and for C-C, C-N, C-O and C-S bond distances. The AM1 and MNDO calculated that N-N, N-O and C=S bond distances are significantly shorter than experimental values due to a systematic error. In general, AM1 ring geometries provide a reliable estimate for the majority of heteroaromatic compounds.</p><p>The Bird I<sub>6</sub> and I<sub>5</sub> aromaticity indices calculated from semiempirical and <em>ab initio</em> geometries are compared with those calculated from experimental bond lengths. None of these semiempirical theoretical methods are successful for rings when the number of heteroatoms exceed the number of carbon atoms. For other heterocycles, AM1 and <em>ab initio</em> 3–21G basis set give the best results, followed by MNDO and then by MINDO/3. Rings containing carbonyl groups are an exception in that MINDO/3 provides the best 16 estimates.</p></div>","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 5","pages":"Pages 247-269"},"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)90102-E","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77330913","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
MOLCONV: A powerful interface program for converting molecule structure files between PC based modeling programs MOLCONV:一个功能强大的界面程序,用于在基于PC的建模程序之间转换分子结构文件
Tetrahedron Computer Methodology Pub Date : 1990-01-01 DOI: 10.1016/0898-5529(90)90076-K
Tamas E. Gunda
{"title":"MOLCONV: A powerful interface program for converting molecule structure files between PC based modeling programs","authors":"Tamas E. Gunda","doi":"10.1016/0898-5529(90)90076-K","DOIUrl":"10.1016/0898-5529(90)90076-K","url":null,"abstract":"<div><p>A molecular input/output data file conversion utility for the IBM PC is presented. The program included on disk in this issue reads and writes the file format of CPSS, Alchemy, Sybyl, Molidea, Desktop MM, PCMODEL, MGP+ modeling software as well as Z-matrix, fractional X-ray and Cartesian coordinates. In addition to conversion, the molecules can be inspected and some geometric data can be calculated. Other utilities are also included.</p></div>","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 6","pages":"Pages 515-522"},"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)90076-K","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89373383","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
Molecular dynamics of associative memory hamiltonians for protein tertiary structure recognition 蛋白质三级结构识别的联想记忆哈密顿子分子动力学
Tetrahedron Computer Methodology Pub Date : 1990-01-01 DOI: 10.1016/0898-5529(90)90051-9
Mark S. Friedrichs, Peter G. Wolynes
{"title":"Molecular dynamics of associative memory hamiltonians for protein tertiary structure recognition","authors":"Mark S. Friedrichs,&nbsp;Peter G. Wolynes","doi":"10.1016/0898-5529(90)90051-9","DOIUrl":"10.1016/0898-5529(90)90051-9","url":null,"abstract":"<div><p>A class of associative memory Hamiltonians for protein tertiary recognition was recently introduced by us. By using a minimization scheme based on molecular dynamics with simulated annealing, we are able to improve and expand upon those initial results. For small proteins lower bound estimates of the Hamiltonians' capacity (the maximum size database for which the Hamiltonian has the ability to reproduce structures) are given; in addition, studies of the dependence of this capacity on various global parameters, such as the choice of sequence encodings, the rate of tolerable mutations in the sequence, and the range of active interactions, are reported. The introduction of the molecular dynamics procedure also permits estimates of the capacity for medium-sized proteins (125–200 residues) to be made. These results demonstrate that the capacity for the simplest realizations of the associative memory Hamiltonians grows as 0.5-0.7N, where N is the number of amino acid residues of the protein to be recalled.</p></div>","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 3","pages":"Pages 175-190"},"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)90051-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89607510","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: 18
Knowledge acquisition from crystallographic databases: Towards a knowledge-based approach to molecular scene analysis 从晶体数据库获取知识:迈向以知识为基础的分子场景分析方法
Tetrahedron Computer Methodology Pub Date : 1990-01-01 DOI: 10.1016/0898-5529(90)90172-5
Frank H. Allen, R. Scott Rowland, Suzanne Fortier , Janice I. Glasgow
{"title":"Knowledge acquisition from crystallographic databases: Towards a knowledge-based approach to molecular scene analysis","authors":"Frank H. Allen,&nbsp;R. Scott Rowland,&nbsp;Suzanne Fortier ,&nbsp;Janice I. Glasgow","doi":"10.1016/0898-5529(90)90172-5","DOIUrl":"10.1016/0898-5529(90)90172-5","url":null,"abstract":"<div><p>Statistical and numerical methods for 3D pattern recognition and classification are now commonly used to acquire structural knowledge from the rapidly growing crystallographic databases. These methods are reviewed, and a semantic network model is described for the storage of crystal and molecular knowledge. The knowledge base is central to an integrated computational strategy for molecular scene analysis: the reconstruction and interpretation of 3D molecular structures and molecular interactions.</p></div>","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 6","pages":"Pages 757-774"},"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)90172-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82086461","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
New regional editorial offices announced 宣布设立新的地区编辑部
Tetrahedron Computer Methodology Pub Date : 1990-01-01 DOI: 10.1016/0898-5529(90)90100-M
{"title":"New regional editorial offices announced","authors":"","doi":"10.1016/0898-5529(90)90100-M","DOIUrl":"https://doi.org/10.1016/0898-5529(90)90100-M","url":null,"abstract":"","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 5","pages":"Page v"},"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)90100-M","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136940756","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
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