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Nurcan Tuncbag et al.
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Sushmita Roy et al.
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A sequence-compatible amount of native burial information is sufficient for determining the structure of small globular proteins
Antonio F. Pereira de Araujo et al.
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John A. Capra et al.
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Wenxu Tong et al.
PLOS COMPUTATIONAL BIOLOGY (2009)
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Andrew J. Bordner
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Protein-protein docking benchmark version 3.0
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OXANA V. GALZITSKAYA et al.
Journal of Bioinformatics and Computational Biology (2008)
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Michal Brylinski et al.
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Julian Mintseris et al.
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Y-h Taguchi et al.
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Brian Pierce et al.
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Michal Brylinski et al.
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Martin Weisel et al.
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Lei Xie et al.
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Nicholas J. Burgoyne et al.
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Looking at enzymes from the inside out: The proximity of catalytic residues to the molecular centroid can be used for detection of active sites and enzyme-ligand interfaces
A Ben-Shimon et al.
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Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites
ATR Laurie et al.
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P Bate et al.
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A new bioinformatic approach to detect common 3D sites in protein structures
M Jambon et al.
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Analysis of accessible surface of residues in proteins
L Lins et al.
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SJ Campbell et al.
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Z Yuan et al.
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ConSurf: Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic Information
F Glaser et al.
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A Pintar et al.
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MS Singer et al.
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MJ Ondrechen et al.
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JL Seffernick et al.
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WZ Li et al.
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GP Brady et al.
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The Protein Data Bank
HM Berman et al.
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