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检索条件"主题词=Protein Data Bank File"
28 条 记 录,以下是1-10 订阅
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PDB4DNA: Implementation of DNA geometry from the protein data bank (PDB) description for Geant4-DNA Monte-Carlo simulations
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COMPUTER PHYSICS COMMUNICATIONS 2015年 192卷 282-288页
作者: Delage, E. Pham, Q. T. Karamitros, M. Payno, H. Stepan, V. Incerti, S. Maigne, L. Perrot, Y. Clermont Univ CNRS IN2P3 Lab Phys Corpusculaire Clermont FerrandLPC F-63171 Aubiere France Univ Bordeaux CENBG Ctr Etudes Nucl Bordeaux Gradignan CNRSIN2P3 F-33175 Gradignan France
This paper describes PDB4DNA, a new Geant4 user application, based on an independent, cross-platform, free and open source C++ library, so-called PDBlib, which enables use of atomic level description of DNA molecule i... 详细信息
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A spatial simulation approach to account for protein structure when identifying non-random somatic mutations
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BMC BIOINFORMATICS 2014年 第1期15卷 1-13页
作者: Ryslik, Gregory A. Cheng, Yuwei Cheung, Kei-Hoi Bjornson, Robert D. Zelterman, Daniel Modis, Yorgo Zhao, Hongyu Yale Sch Publ Hlth Dept Biostat New Haven CT 06520 USA Yale Univ Program Computat Biol & Bioinformat New Haven CT 06520 USA Yale Sch Med Yale Ctr Med Informat New Haven CT USA Yale Univ Dept Comp Sci New Haven CT 06520 USA Yale Univ Dept Mol Biophys & Biochem New Haven CT 06520 USA
Background: Current research suggests that a small set of "driver" mutations are responsible for tumorigenesis while a larger body of "passenger" mutations occur in the tumor but do not progress th... 详细信息
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MUFOLD-DB: a processed protein structure database for protein structure prediction and analysis
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BMC GENOMICS 2014年 第11-Sup期15卷 1-7页
作者: He, Zhiquan Zhang, Chao Xu, Yang Zeng, Shuai Zhang, Jingfen Xu, Dong Univ Missouri Dept Comp Sci Columbia MO 65211 USA Univ Missouri CS Bond Life Sci Ctr Columbia MO 65211 USA
Background: protein structure data in protein data bank (PDB) are widely used in studies of protein function and evolution and in protein structure prediction. However, there are two main barriers in large-scale usage... 详细信息
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Prediction of RNA-binding amino acids from protein and RNA sequences
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BMC BIOINFORMATICS 2011年 第s13期12卷 1-12页
作者: Choi, Sungwook Han, Kyungsook Inha Univ Sch Comp Sci & Engn Inchon 402751 South Korea
Background: Many learning approaches to predicting RNA-binding residues in a protein sequence construct a non-redundant training dataset based on the sequence similarity. The sequence similarity-based method either ta... 详细信息
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BUDDY-system: A web site for constructing a dataset of protein pairs between ligand-bound and unbound states
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BMC Research Notes 2011年 第1期4卷 1-4页
作者: Morita, Mizuki Terada, Tohru Nakamura, Shugo Shimizu, Kentaro Department of Fundamental Research National Institute of Biomedical Innovation (NIBIO) Ibaraki Osaka 567-0085 7-6-8 Saito Asagi Japan Institute for Bioinformatics Research and Development (BIRD) Japan Science and Technology Agency (JST) Kawaguchi Saitama 332-0012 4-1-8 Honcho Japan Agricultural Bioinformatics Research Unit University of Tokyo Bunkyo Tokyo 113-8657 1-1-1 Yayoi Japan Department of Biotechnology University of Tokyo Bunkyo Tokyo 113-8657 1-1-1 Yayoi Japan
Background: Elucidating molecular recognition by proteins, such as in enzyme-substrate and receptor-ligand interactions, is a key to understanding biological phenomena. To delineate these protein interactions, it is i... 详细信息
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Hydrophobic pulses predict transmembrane helix irregularities and channel transmembrane units
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BMC BIOINFORMATICS 2011年 第1期12卷 1-10页
作者: Paulet, Damien Claustres, Mireille Beroud, Christophe Univ Montpellier I Montpellier France INSERM U827 Montpellier France Hop Arnaud de Villeneuve Lab Genet Mol CHU Montpellier Montpellier France
Background: Few high-resolution structures of integral membranes proteins are available, as crystallization of such proteins needs yet to overcome too many technical limitations. Nevertheless, prediction of their tran... 详细信息
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Predicting DNA-binding locations and orientation on proteins using knowledge-based learning of geometric properties
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PROTEOME SCIENCE 2011年 第1-Sup期9卷 S11-S11页
作者: Wang, Chien-Chih Chen, Chien-Yu Natl Taiwan Univ Dept Bioind Mechatron Engn Taipei 106 Taiwan Natl Taiwan Univ Dept Comp Sci & Informat Engn Taipei 106 Taiwan
Background: DNA-binding proteins perform their functions through specific or non-specific sequence recognition. Although many sequence-or structure-based approaches have been proposed to identify DNA-binding residues ... 详细信息
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EasyModeller: A graphical interface to MODELLER
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BMC Research Notes 2010年 第1期3卷 1-5页
作者: Kuntal, Bhusan K Aparoy, Polamarasetty Reddanna, Pallu School of Life Sciences University of Hyderabad Hyderabad 500 046 India
Background. MODELLER is a program for automated protein Homology Modeling. It is one of the most widely used tool for homology or comparative modeling of protein three-dimensional structures, but most users find it a ... 详细信息
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Potentials 'R'Us web-server for protein energy estimations with coarse-grained knowledge-based potentials
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BMC BIOINFORMATICS 2010年 第1期11卷 92-92页
作者: Feng, Yaping Kloczkowski, Andrzej Jernigan, Robert L. Iowa State Univ Dept Biochem Biophys & Mol Biol Ames IA 50011 USA Iowa State Univ LH Baker Ctr Bioinformat & Biol Stat Ames IA 50011 USA
Background: Knowledge-based potentials have been widely used in the last 20 years for fold recognition, protein structure prediction from amino acid sequence, ligand binding, protein design, and many other purposes. H... 详细信息
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The protein-DNA Interface database
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BMC BIOINFORMATICS 2010年 第1期11卷 262-262页
作者: Norambuena, Tomas Melo, Francisco Pontificia Univ Catolica Chile Fac Ciencias Biol Dept Mol Genet & Microbiol Santiago Chile
The protein-DNA Interface database (PDIdb) is a repository containing relevant structural information of protein-DNA complexes solved by X-ray crystallography and available at the protein data bank. The database inclu... 详细信息
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