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The Extended Version of the Computer Package CST for Conversions, Standardization and Transformations of the Spin Hamiltonian and the Crystal-field Hamiltonian 自旋哈密顿量和晶体场哈密顿量的转换、标准化和变换计算机包CST的扩展版本
Computers & chemistry Pub Date : 2002-01-01 DOI: 10.1016/S0097-8485(01)00092-4
C. Rudowicz, Qin Jian
{"title":"The Extended Version of the Computer Package CST for Conversions, Standardization and Transformations of the Spin Hamiltonian and the Crystal-field Hamiltonian","authors":"C. Rudowicz, Qin Jian","doi":"10.1016/S0097-8485(01)00092-4","DOIUrl":"https://doi.org/10.1016/S0097-8485(01)00092-4","url":null,"abstract":"","PeriodicalId":79331,"journal":{"name":"Computers & chemistry","volume":"75 1","pages":"149-57"},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83298939","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: 40
Artificial neural network model for predicting protein subcellular location 预测蛋白质亚细胞定位的人工神经网络模型
Computers & chemistry Pub Date : 2002-01-01 DOI: 10.1016/S0097-8485(01)00106-1
Yu-Dong Cai , Xiao-Jun Liu , Kuo-Chen Chou
{"title":"Artificial neural network model for predicting protein subcellular location","authors":"Yu-Dong Cai ,&nbsp;Xiao-Jun Liu ,&nbsp;Kuo-Chen Chou","doi":"10.1016/S0097-8485(01)00106-1","DOIUrl":"https://doi.org/10.1016/S0097-8485(01)00106-1","url":null,"abstract":"<div><p>The function of a protein is closely correlated to its subcellular location. Is it possible to utilize a bioinformatics method to predict the protein subcellular location? To explore this problem, proteins are classified into 12 groups (Protein Eng. 12 (1999) 107–118) according to their subcellular location: (1) chloroplast, (2) cytoplasm, (3) cytoskeleton, (4) endoplasmic reticulum, (5) extracellular, (6) Golgi apparatus, (7) lysosome, (8) mitochondria, (9) nucleus, (10) peroxisome, (11) plasma membrane and (12) vacuole. In this paper, the neural network method was proposed to predict the subcellular location of a protein according to its amino acid composition. Results obtained through self-consistency, cross-validation and independent dataset tests are quite high. Accordingly, the present method can serve as a complement tool for the existing prediction methods in this area.</p></div>","PeriodicalId":79331,"journal":{"name":"Computers & chemistry","volume":"26 2","pages":"Pages 179-182"},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0097-8485(01)00106-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91666155","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: 33
A subset-orientated algorithm for minimizing the number of steps required for synthesis of cyclic-peptide libraries 一种面向子集的算法，用于最小化合成环肽库所需的步骤数
Computers & chemistry Pub Date : 2002-01-01 DOI: 10.1016/S0097-8485(01)00087-0
Tran Trung Tran , Darryn Bryant , Mark Smythe
{"title":"A subset-orientated algorithm for minimizing the number of steps required for synthesis of cyclic-peptide libraries","authors":"Tran Trung Tran ,&nbsp;Darryn Bryant ,&nbsp;Mark Smythe","doi":"10.1016/S0097-8485(01)00087-0","DOIUrl":"https://doi.org/10.1016/S0097-8485(01)00087-0","url":null,"abstract":"<div><p>Libraries of cyclic peptides are being synthesized using combinatorial chemistry for high throughput screening in the drug discovery process. This paper describes the min_syn_steps.cpp program (available at <span>http://www.imb.uq.edu.au/groups/smythe/tran</span><svg><path></path></svg>), which after inputting a list of cyclic peptides to be synthesized, removes cyclic redundant sequences and calculates synthetic strategies which minimize the synthetic steps as well as the reagent requirements. The synthetic steps and reagent requirements could be minimized by finding common subsets within the sequences for block synthesis. Since a brute-force approach to search for optimum synthetic strategies is impractically large, a subset-orientated approach is utilized here to limit the size of the search.</p></div>","PeriodicalId":79331,"journal":{"name":"Computers & chemistry","volume":"26 2","pages":"Pages 113-117"},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0097-8485(01)00087-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91666157","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
Artificial Neural Network Model for Predicting Protein Subcellular Location 预测蛋白质亚细胞定位的人工神经网络模型
Computers & chemistry Pub Date : 2002-01-01 DOI: 10.1016/S0097-8485(01)00106-1
Yu-Dong Cai, Xiao-Jun Liu, K. Chou
{"title":"Artificial Neural Network Model for Predicting Protein Subcellular Location","authors":"Yu-Dong Cai, Xiao-Jun Liu, K. Chou","doi":"10.1016/S0097-8485(01)00106-1","DOIUrl":"https://doi.org/10.1016/S0097-8485(01)00106-1","url":null,"abstract":"","PeriodicalId":79331,"journal":{"name":"Computers & chemistry","volume":"45 1","pages":"179-82"},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80267385","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
The extended version of the computer package CST for conversions, standardization and transformations of the spin Hamiltonian and the crystal-field Hamiltonian 计算机包CST的扩展版本，用于自旋哈密顿量和晶体场哈密顿量的转换，标准化和转换
Computers & chemistry Pub Date : 2002-01-01 DOI: 10.1016/S0097-8485(01)00092-4
C. Rudowicz, Q. Jian
{"title":"The extended version of the computer package CST for conversions, standardization and transformations of the spin Hamiltonian and the crystal-field Hamiltonian","authors":"C. Rudowicz,&nbsp;Q. Jian","doi":"10.1016/S0097-8485(01)00092-4","DOIUrl":"https://doi.org/10.1016/S0097-8485(01)00092-4","url":null,"abstract":"<div><p>The computer package CST (Conversions, Standardization and Transformations) is useful for general manipulations of the zero-field splitting (ZFS) and crystal field (CF) parameters for various systems, especially for transition ions at orthorhombic and lower symmetry sites in crystals. The ZFS parameters are extensively used in the EMR and related spectroscopic and magnetic studies (e.g. magnetic susceptibility, magnetic anisotropy, Mössbauer spectroscopy), whereas the CF parameters in optical absorption spectroscopy, inelastic neutron scattering, and infrared spectroscopy. An extended version of the CST package developed recently is presented in this paper. The standardization, including the standardization errors, for the five possible non-standard ranges of the ‘rhombicity’ parameter for monoclinic and triclinic symmetry in the local axis system has been worked out. The handling of the border points in the standardization module has been improved. The rotational invariants used before only for the transformations of the CF parameters have been incorporated into the standardization module for the CF and ZFS parameters expressed in any of the major tensor operator notations. The input option in the Euler angles has been added into the transformation module, and the newest physical constants in the unit conversions module have been adopted. Specific applications of the CST package for the CF and ZFS parameters will be presented elsewhere.</p></div>","PeriodicalId":79331,"journal":{"name":"Computers & chemistry","volume":"26 2","pages":"Pages 149-157"},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0097-8485(01)00092-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91622398","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: 40
Theoretical Study of the Internal Rotational Barriers in Nitrotoluenes, Nitrophenols, and Nitroanilines 硝基甲苯、硝基酚和硝基苯胺内部旋转势垒的理论研究
Computers & chemistry Pub Date : 2002-01-01 DOI: 10.1016/S0097-8485(01)00105-X
P. Chen, S. C. Chen
{"title":"Theoretical Study of the Internal Rotational Barriers in Nitrotoluenes, Nitrophenols, and Nitroanilines","authors":"P. Chen, S. C. Chen","doi":"10.1016/S0097-8485(01)00105-X","DOIUrl":"https://doi.org/10.1016/S0097-8485(01)00105-X","url":null,"abstract":"","PeriodicalId":79331,"journal":{"name":"Computers & chemistry","volume":"4 1","pages":"171-8"},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89958696","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: 19
Theoretical study of the morphologically originated noise associated with the transmittance of a precipitation system 与降水系统透光率有关的形态源噪声的理论研究
Computers & chemistry Pub Date : 2002-01-01 DOI: 10.1016/S0097-8485(01)00090-0
J.A. Poce-Fatou, R. Alcántara, J. Martı́n
{"title":"Theoretical study of the morphologically originated noise associated with the transmittance of a precipitation system","authors":"J.A. Poce-Fatou,&nbsp;R. Alcántara,&nbsp;J. Martı́n","doi":"10.1016/S0097-8485(01)00090-0","DOIUrl":"https://doi.org/10.1016/S0097-8485(01)00090-0","url":null,"abstract":"<div><p>In this paper we present the results of a computational study that analyses the relationship between the noise associated with the optical transmittance of a system of particles and the morphology of such particles. Computational algorithms have been developed in order to represent the different morphologies within a wide range of sizes. By using this methodology, it has been possible to study the morphology of particles in a virtual system, therefore avoiding the distortions that would inevitably be present in a real system. As a consequence of this study, a classification of the morphologies observed has been made according to the amount of noise they would add to the transmittance of a system of particles. The theoretical results obtained are in good agreement with the available experimental data obtained in real systems.</p></div>","PeriodicalId":79331,"journal":{"name":"Computers & chemistry","volume":"26 2","pages":"Pages 131-140"},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0097-8485(01)00090-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90011478","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
A Subset-orientated Algorithm for Minimizing the Number of Steps Required for Synthesis of Cyclic-peptide Libraries 一种面向子集的环状肽库合成步骤最小化算法
Computers & chemistry Pub Date : 2002-01-01 DOI: 10.1016/S0097-8485(01)00087-0
T. T. Tran, D. Bryant, M. Smythe
{"title":"A Subset-orientated Algorithm for Minimizing the Number of Steps Required for Synthesis of Cyclic-peptide Libraries","authors":"T. T. Tran, D. Bryant, M. Smythe","doi":"10.1016/S0097-8485(01)00087-0","DOIUrl":"https://doi.org/10.1016/S0097-8485(01)00087-0","url":null,"abstract":"","PeriodicalId":79331,"journal":{"name":"Computers & chemistry","volume":"195 1","pages":"113-7"},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79846027","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
The study on automorphism group of ESESOC ESESOC的自同构群研究
Computers & chemistry Pub Date : 2002-01-01 DOI: 10.1016/S0097-8485(01)00089-4
Jun-Feng Hao, Lu Xu
{"title":"The study on automorphism group of ESESOC","authors":"Jun-Feng Hao,&nbsp;Lu Xu","doi":"10.1016/S0097-8485(01)00089-4","DOIUrl":"10.1016/S0097-8485(01)00089-4","url":null,"abstract":"<div><p>It is necessary to generate the automorphism group of a chemical graph in computer-aided structure elucidation. In this paper, an algorithm was developed by the all-paths topological symmetry algorithm to build the automorphism group of a chemical graph. A comparison of several topological symmetry algorithms reveals that the all-paths algorithm (APA) could yield the correct class of a chemical graph. It lays a foundation for the ESESOC system in computer-aided structure elucidation.</p></div>","PeriodicalId":79331,"journal":{"name":"Computers & chemistry","volume":"26 2","pages":"Pages 119-123"},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0097-8485(01)00089-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86545839","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
Consistent integration of non-reliable heterogeneous information resources applied to the annotation of transmembrane proteins 非可靠异构信息资源的一致整合应用于跨膜蛋白的注释
Computers & chemistry Pub Date : 2001-12-01 DOI: 10.1016/S0097-8485(01)00098-5
Steffen Möller , Michael Schroeder , Rolf Apweiler
{"title":"Consistent integration of non-reliable heterogeneous information resources applied to the annotation of transmembrane proteins","authors":"Steffen Möller ,&nbsp;Michael Schroeder ,&nbsp;Rolf Apweiler","doi":"10.1016/S0097-8485(01)00098-5","DOIUrl":"10.1016/S0097-8485(01)00098-5","url":null,"abstract":"<div><p>Information agents integrate multiple distributed heterogeneous information sources. The challenging yet unsolved problem that remains, is to ensure the semantic consistency of the integrated data. In this paper we set out to develop a general approach to inconsistency management for information agents. It is implemented as part of the EDITtoTrEMBL system and applied on a large real-world problem in the domain of bioinformatics.</p></div>","PeriodicalId":79331,"journal":{"name":"Computers & chemistry","volume":"26 1","pages":"Pages 41-49"},"PeriodicalIF":0.0,"publicationDate":"2001-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0097-8485(01)00098-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75812961","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: 16
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