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CORE:Common Region Extension Based Multiple Protein structure alignment for Producing Multiple Solution

Journal of Computer Science & Technology 2013年第4期28卷 647-656页

作者： Woo-Cheol Kim Sanghyun Park Jung-Im Won College of Information Sciences and Technology The Pennsylvania State University University Park Department of Computer Science Yonsei University Research Center of Information and Electronic Engineering Hallym University Chuncheon

Over the past several decades, biologists have conducted numerous studies examining both general and specific functions of proteins. Generally, if similarities in either the structure or sequence of amino acids exist for two proteins, then a common biological function is expected. Protein function is determined primarily based on the structure rather than the sequence of amino acids. The algorithm for protein structure alignment is an essential tool for the research. The quality of the algorithm depends on the quality of the similarity measure that is used, and the similarity measure is an objective function used to determine the best alignment because of their individual strength and weakness However, none of existing similarity measures became golden standard They require excessive filtering to find a single alignment. In this paper, we introduce a new strategy that finds not a single alignment, but multiple alignments with different lengths. This method has obvious benefits of high quality alignment. However, this novel method leads to a new problem that the running time for this method is considerably longer than that for methods that find only a single alignment. To address this problem~ we propose algorithms that can locate a common region （CORE） of multiple alignment candidates, and can then extend the CORE into multiple alignments. Because the CORE can be defined from a final alignment, we introduce CORE＊ that is similar to CORE and propose an algorithm to identify the CORE＊. By adopting CORE＊ and dynamic programming, our proposed method produces multiple alignments of various lengths with higher accuracy than previous methods. In the experiments, the alignments identified by our algorithm are longer than those obtained by TM-align by 17% and 15.48%, on average, when the comparison is conducted at the level of super-family and fold, respectively.

关键词： structure alignment similarity search protein structure

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RM-structure alignment based statistical machine translation model

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High Technology Letters 2008年第3期14卷 271-275页

作者：孙加东 Zhao Tiejun MOE-MS Key Laboratory of Natural Language Processing and Speech Harbin Institute of Technology Harbin 150001 P.R. China

A novel model based on structure alignments is proposed for statistical machine translation in this paper. Meta-structure and sequence of meta-structure for a parse tree are defined. During the translation process, a parse tree is decomposed to deal with the structure divergence and the alignments can be constructed at different levels of recombination of meta-structure （RM）. This method can perform the structure mapping across the sub-tree structure between languages. As a result, we get not only the translation for the target language, but sequence of meta-stmctu .re of its parse tree at the same time. Experiments show that the model in the framework of log-linear model has better generative ability and significantly outperforms Pharaoh, a phrase-based system.

关键词： statistical machine translation recombination of meta-structure ( RM) structure alignment log-linear model

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FP-Zernike:An Open-source Structural Database Construction Toolkit for Fast structure Retrieval

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Genomics, Proteomics & Bioinformatics 2024年第1期22卷 111-119页

作者： Junhai Qi Chenjie Feng Yulin Shi Jianyi Yang Fa Zhang Guojun Li Renmin Han Research Center for Mathematics and Interdisciplinary Sciences Shandong UniversityQingdao 266237China BioMap Research Menlo ParkCA 94025USA College of Medical Information and Engineering Ningxia Medical UniversityYinchuan 750004China Institute of Engineering Medicine Beijing Institute of TechnologyBeijing 100081China

The release of AlphaFold2 has sparked a rapid expansion in protein model *** protein structure retrieval is crucial for the analysis of structure models,while measuring the similarity between structures is the key challenge in structural *** existing structure alignment algorithms can address this challenge,they are often ***,the state-of-the-art approach involves converting protein structures into three-dimensional(3D)Zernike descriptors and assessing similarity using Euclidean ***,the methods for computing 3D Zernike descriptors mainly rely on structural surfaces and are predominantly web-based,thus limiting their application in studying custom *** overcome this limitation,we developed FP-Zernike,a user-friendly toolkit for computing different types of Zernike descriptors based on feature *** simply need to enter a single line of command to calculate the Zernike descriptors of all structures in customized ***-Zernike outperforms the leading method in terms of retrieval accuracy and binary classification accuracy across diverse benchmark *** addition,we showed the application of FP-Zernike in the construction of the descriptor database and the protocol used for the Protein Data Bank(PDB)dataset to facilitate the local deployment of this tool for interested *** demonstration contained 590,685 structures,and at this scale,our system required only 4-9 s to complete a *** experiments confirmed that it achieved the state-of-the-art accuracy ***-Zernike is an open-source toolkit,with the source code and related data accessible at https://***/biocode/tools/BT007365/releases/0.1,as well as through a webserver at http://***/.

关键词： Zernike descriptor structure alignment PDB dataset Open-source Retrieval system

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A DIFFERENTIAL GEOMETRIC APPROACH TO PROTEIN STRUTURE alignment

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生物数学学报 1993年第1期 1-17页

作者： Ding Dafu and Feng Zukang (Shanghai Institute of Biochemistry, Academia sinica 200031)

A new method of comparing protein structures is deseribed, based on the differential-geometric representaion of protein conformation with the information of global dissimilarity and residue *** utility of this method for comparing closely and distantly related homologous proteins is demostrated by multiple alignment of globins, serine proteinases and aspartic proteinases.

关键词： Protein conformation Curvature and torsion of protein backbone structure alignment dynamic programming

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Clustering dendrograms construction and analysis of TIM-barrel proteins by structure information

Clustering dendrograms construction and analysis of TIM-barr...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Xin-Rui SONG Xiao-Qin LI Bioengineering Center Beijing University of Technology

Background:The regularity study of protein molecular evolution is the key to molecular evolution and it has important meaning to reveal life origin and the evolutionary mechanism. TIM-barrel fold is a typical fold type and members of this fold have a common topology but with little sequence similarity through *** pairwise amino acid sequence diversity of TIM-barrel fold proteins can be up to 70%,so it is difficult to detect their evolutionary relationship from *** a result of the growing number of protein structure information of PDB and the development of structure alignment algorithms,basing on structure comparison make it better to study TIM-barrel fold proteins than that of sequence. Methods:In this paper,326 TIM-barrel proteins with the spatial structure material and known species information were selected from Astral 1.65(sequence identity structure alignment information,*** species phylogenies of different datasets were obtained from NCBI. Results:The analysis about clustering dendrograms of TIM-barrel protein dataset shows that proteins with similar function obviously tend to *** same superfamily members are almost clustered in a large branch and the same family members are clustered in a small branch belonging to their superfamily’***,there is little relation between clustering dendrograms and their corresponding species *** analysis of other three subsets indicates that under the constraints of function,clustering dendrograms of TIM-barrel proteins have a good corresponding relation with species phylogenies. Conclusions:Our results indicate that the structure evolution of TIM-barrel proteins reflects the constraints of protein function,the structural differences between specific functional TIM-

关键词： TIM-barrel proteins structure alignment hierarchical cluster species evolution

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