Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003最新文献_第2页

New computational methods for electrostatics in macromolecular simulation 大分子模拟中静电的新计算方法

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227371

I. Tsukerman

引用次数: 2

Riptide: fast protein identification from mass spectrometer data 激流:快速蛋白质鉴定从质谱仪数据

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227344

R. Carter

引用次数: 1

Multiple protein structure alignment by deterministic annealing 基于确定性退火的多蛋白结构比对

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227421

Luonan Chen

{"title":"Multiple protein structure alignment by deterministic annealing","authors":"Luonan Chen","doi":"10.1109/CSB.2003.1227421","DOIUrl":"https://doi.org/10.1109/CSB.2003.1227421","url":null,"abstract":"In this paper, we propose a novel method for solving multiple structure alignment problem, based on mean field annealing technique. We define the structure alignment as a mixed integer-programming (MIP) problem with the inter-atomic distances between two or more structures as an objective function[1]. The integer variables represent the marchings among structures whereas the continuous variables are translation vectors and rotation matrices with each protein structure as a rigid body. By exploiting the special structure of continuous partial problem, we transform the MIP into a nonlinear optimization problem (NOP) with a nonlinear objective function and linear constraints, based on mean field equations. To optimize the NOP, a mean field annealing procedure is adopted with a modified Potts spin model[2]. Since all linear constraints are embedded in the mean field equations, we do not need to add any penalty terms of the constraints to the error function. In other words, there is no \"soft constraint\" in our mean field model and all constraints are automatically satisfied during the annealing process, thereby not only making the optimization more efficiently but also eliminating unnecessary parameters of penalty that usually require careful tuning dependent on the problems.","PeriodicalId":147883,"journal":{"name":"Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003","volume":"PP 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2003-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126356120","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: 38

Two operative concepts for the post-genomic era: the "memoire vive" of the cell and a molecular algebra 后基因组时代的两个操作概念:细胞的“活记忆”和分子代数

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227310

S. Bentolila

引用次数: 2

On gene prediction by cross-species comparative sequence analysis 跨物种比较序列分析的基因预测

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227366

Rong Chen, H. Ali

引用次数: 0

GenericBioMatch: A novel generic pattern match algorithm for biological sequences GenericBioMatch:一种新的生物序列通用模式匹配算法

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227408

Youlian Pan, Fazel Famili

引用次数: 1

Local minima-based exploration for off-lattice protein folding 基于局部最小的非晶格蛋白质折叠探索

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227424

E. Santos, K. Kim, Eunice E. Santos

{"title":"Local minima-based exploration for off-lattice protein folding","authors":"E. Santos, K. Kim, Eunice E. Santos","doi":"10.1109/CSB.2003.1227424","DOIUrl":"https://doi.org/10.1109/CSB.2003.1227424","url":null,"abstract":"We present a new and simple algorithmic approach to help predict protein structures from amino acid sequences based on energy minimization. In the search for the minimal energy conformation, we analyze and exploit the protein structures found at the various local minima to direct the search the global minimum. As such, we explore the energy landscape efficiently by considering only the space of local minima instead of the whole feasible space of conformations. Our specific algorithmic approach is comprised of two different elements: local minimization and operators from genetic algorithms. Unlike existing hybrid approaches where the local optimization is used to fine-tune the solutions, we focus primarily on the local optimization and employ stochastic sampling through genetic operators for diversification. Our empirical results indicate that each local minimum is representative of the substructures contained in the set of solutions surrounding the local minima. We applied our approach to determining the minimal energy conformation of proteins from the protein data bank (PDB) using the CHARMM and UNRES energy model. We compared against standard genetic algorithms and Monte Carlo approaches as well as the conformations found in the PDB as the baseline. In all cases, our new approach computed the lowest energy conformation.","PeriodicalId":147883,"journal":{"name":"Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003","volume":"39 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2003-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131929741","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

Identifying gene and protein names from biological texts 从生物学文本中识别基因和蛋白质名称

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227431

Weijian Xuan, S. Watson, H. Akil, F. Meng

引用次数: 7

SNP analysis system for detecting complex disease associated sites 用于检测复杂疾病相关位点的SNP分析系统

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227368

Yoko Higashi, Hirotaka Higuchi, T. Kido, Hirohito Matsumine, Masanori Baba, Toshihiko Morimoto, Masaaki Muramatsu

{"title":"SNP analysis system for detecting complex disease associated sites","authors":"Yoko Higashi, Hirotaka Higuchi, T. Kido, Hirohito Matsumine, Masanori Baba, Toshihiko Morimoto, Masaaki Muramatsu","doi":"10.1109/CSB.2003.1227368","DOIUrl":"https://doi.org/10.1109/CSB.2003.1227368","url":null,"abstract":"We developed a system that supports disease association studies to detect genes that may cause complex diseases. The main function of the system is to examine the possibility of each polymorphism being associated with a disease. Another important function is to perform linkage disequilibrium analysis and combine SNPs (single nucleotide polymorphisms) together into LDblocks (linkage-disequilibrium-blocks) to improve statistical power for association study. Those analyses can be efficiently performed using an analysis pipeline of the new system with handy tools for eliminating the inadequate data and so on. Consequently, the number of SNPs the system can analyze is about 30 to 50 times higher than by the standard manual procedures per unit of time. The new system also has a sophisticated visualization tool. The main viewer displays the genomic structure and is linked to another main viewer showing the in-depth analysis result. These viewers let the user easily check and make an interpretation of the results. The new system should provide significant assistance for the genome research of complex diseases.","PeriodicalId":147883,"journal":{"name":"Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003","volume":"36 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2003-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133806663","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

Genomic sequence analysis using gap sequences and pattern filtering 基因组序列分析使用间隙序列和模式滤波

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227401

Shih-Chieh Su, C. Yeh, C.-C. Jay Kuo

引用次数: 1