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    MJ
    2008
    98views more  MJ 2008»
    Prototyping bio-nanorobots using molecular dynamics simulation and virtual reality
    14 years 12 days ago
    Prototyping bio-nanorobots using molecular dynamics simulation and virtual reality
    Download  www.coe.neu.edu
    This paper presents a molecular mechanics study using a molecular dynamics software (NAMD) coupled to virtual reality (VR) techniques for intuitive bio-nanorobotic prototyping. Us...
    Mustapha Hamdi, Antoine Ferreira, Gaurav Sharma, C...
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    JIB
    2006
    106views more  JIB 2006»
    A structural keystone for drug design
    14 years 12 days ago
    A structural keystone for drug design
    Download  userpage.chemie.fu-berlin.de
    3D-structures of proteins and potential ligands are the cornerstones of rational drug design. The first brick to build upon is selecting a protein target and finding out whether b...
    Kristian Rother, Mathias Dunkel, Elke Michalsky, S...
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    JCB
    2006
    215views more  JCB 2006»
    Protein Fold Recognition Using Segmentation Conditional Random Fields (SCRFs)
    14 years 12 days ago
    Protein Fold Recognition Using Segmentation Conditional Random Fields (SCRFs)
    Download  www.cs.cmu.edu
    Protein fold recognition is an important step towards understanding protein three-dimensional structures and their functions. A conditional graphical model, i.e., segmentation con...
    Yan Liu 0002, Jaime G. Carbonell, Peter Weigele, V...
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    JCC
    2008
    92views more  JCC 2008»
    Fast procedure for reconstruction of full-atom protein models from reduced representations
    14 years 12 days ago
    Fast procedure for reconstruction of full-atom protein models from reduced representations
    Download  cssb.biology.gatech.edu
    : We introduce PULCHRA, a fast and robust method for the reconstruction of full-atom protein models starting from a reduced protein representation. The algorithm is particularly su...
    Piotr Rotkiewicz, Jeffrey Skolnick
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    JCC
    2008
    110views more  JCC 2008»
    On the structure of the inverse kinematics map of a fragment of protein backbone
    14 years 12 days ago
    On the structure of the inverse kinematics map of a fragment of protein backbone
    Download  ai.stanford.edu
    Loop closure in proteins requires computing the values of the inverse kinematics (IK) map for a backbone fragment with 2n 6 torsional degrees of freedom (dofs). It occurs in a va...
    R. James Milgram, Guanfeng Liu, Jean-Claude Latomb...
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    JBI
    2008
    137views Bioinformatics» more  JBI 2008»
    Mining sequential patterns for protein fold recognition
    14 years 12 days ago
    Mining sequential patterns for protein fold recognition
    Download  medlab.cs.uoi.gr
    Protein data contain discriminative patterns that can be used in many beneficial applications if they are defined correctly. In this work sequential pattern mining (SPM) is utiliz...
    Themis P. Exarchos, Costas Papaloukas, Christos La...
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    BMCBI
    2007
    115views more  BMCBI 2007»
    Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites
    14 years 13 days ago
    Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites
    Download  www.biomedcentral.com
    Background: We performed an exhaustive search for local structural similarities in an ensemble of non-redundant protein functional sites. With the purpose of finding new examples ...
    Gabriele Ausiello, Daniele Peluso, Allegra Via, Ma...
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    BMCBI
    2007
    93views more  BMCBI 2007»
    SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition
    14 years 13 days ago
    SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition
    Download  noble.gs.washington.edu
    Background: Predicting a protein’s structural class from its amino acid sequence is a fundamental problem in computational biology. Much recent work has focused on developing ne...
    Iain Melvin, Eugene Ie, Rui Kuang, Jason Weston, W...
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    BMCBI
    2007
    142views more  BMCBI 2007»
    LinkHub: a Semantic Web system that facilitates cross-database queries and information retrieval in proteomics
    14 years 13 days ago
    LinkHub: a Semantic Web system that facilitates cross-database queries and information retrieval in proteomics
    Download  www.biomedcentral.com
    nd: A key abstraction in representing proteomics knowledge is the notion of unique identifiers for individual entities (e.g. proteins) and the massive graph of relationships among...
    Andrew K. Smith, Kei-Hoi Cheung, Kevin Y. Yip, Mar...
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    BMCBI
    2007
    116views more  BMCBI 2007»
    Clustering protein environments for function prediction: finding PROSITE motifs in 3D
    14 years 13 days ago
    Clustering protein environments for function prediction: finding PROSITE motifs in 3D
    Download  www.biomedcentral.com
    Background: Structural genomics initiatives are producing increasing numbers of threedimensional (3D) structures for which there is little functional information. Structure-based ...
    Sungroh Yoon, Jessica C. Ebert, Eui-Young Chung, G...
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