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Proteins, v.84, 2016년, pp.293 - 301
Lee, Gyu Rie (Department of Chemistry, Seoul National University, Seoul, 151‐) , Heo, Lim (747, Republic of Korea) , Seok, Chaok (Department of Chemistry, Seoul National University, Seoul, 151‐)
EDISON 유발 논문
계산과학플랫폼 EDISON을 활용하여 발표된 논문국가컴퓨팅센터 유발 논문
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ABSTRACTProtein structures predicted by state‐of‐the‐art template‐based methods may still have errors when the template proteins are not similar enough to the target protein. Overall target structure may deviate from the template structures owing to differences in sequences. ...
Zhang Y. Protein structure prediction: when is it useful? Curr Opin Struct Biol 2009 ; 19 : 145 – 155 .
Cavasotto CN , Phatak SS. Homology modeling in drug discovery: current trends and applications . Drug Discov Today 2009 ; 14 : 676 – 683 .
Giorgetti A , Raimondo D , Miele AE , Tramontano A. Evaluating the usefulness of protein structure models for molecular replacement . Bioinformatics 2005 ; 21 ( Suppl 2 ): ii72 – 76 .
Martí‐Renom MA , Stuart AC , Fiser A , Sánchez R , Melo F , Sali A. Comparative protein structure modeling of genes and genomes . Annu Rev Biophys Biomol Struct 2000 ; 29 : 291 – 325 .
Baker D , Sali A. Protein structure prediction and structural genomics . Science 2001 ; 294 : 93 – 96 .
Zhang Y. Progress and challenges in protein structure prediction . Curr Opin Struct Biol 2008 ; 18 : 342 – 348 .
Lee MR , Tsai J , Baker D , Kollman PA. Molecular dynamics in the endgame of protein structure prediction . J Mol Biol 2001 ; 313 : 417 – 430 .
Chen JH , Brooks CL. Can molecular dynamics simulations provide high‐resolution refinement of protein structure? Proteins 2007 ; 67 : 922 – 930 .
Ishitani R , Terada T , Shimizu K. Refinement of comparative models of protein structure by using multicanonical molecular dynamics simulations . Mol Simulat 2008 ; 34 : 327 – 336 .
Raval A , Piana S , Eastwood MP , Dror RO , Shaw DE. Refinement of protein structure homology models via long, all‐atom molecular dynamics simulations . Proteins 2012 ; 80 : 2071 – 2079 .
Mirjalili V , Feig M. Protein structure refinement through structure selection and averaging from molecular dynamics ensembles . J Chem Theory Comput 2013 ; 9 : 1294 – 1303 .
Mirjalili V , Noyes K , Feig M. Physics‐based protein structure refinement through multiple molecular dynamics trajectories and structure averaging . Proteins 2014 ; 82 : 196 – 207 .
Chopra G , Summa CM , Levitt M. Solvent dramatically affects protein structure refinement . Proc Natl Acad Sci U S A 2008 ; 105 : 20239 – 20244 .
Fan H , Mark AE. Refinement of homology‐based protein structures by molecular dynamics simulation techniques . Protein Sci 2004 ; 13 : 211 – 220 .
Cornell WD , Cieplak P , Bayly CI , Gould IR , Merz KM , Ferguson DM , Spellmeyer DC , Fox T , Caldwell JW , Kollman PA. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules (1995, 117, 5179‐5197) . J Am Chem Soc 1996 ; 118 : 2309 – 2309 .
Best RB , Zhu X , Shim J , Lopes PEM , Mittal J , Feig M , MacKerell AD. Optimization of the additive CHARMM all‐atom protein force field targeting improved sampling of the backbone φ, ψ and side‐chain χ(1) and χ(2) dihedral angles . J Chem Theory Comput 2012 ; 8 : 3257 – 3273 .
Jorgensen WL , Maxwell DS , Tirado‐Rives J. Development and testing of the OPLS all‐atom force field on conformational energetics and properties of organic liquids . J Am Chem Soc 1996 ; 118 : 11225 – 11236 .
Kaminski GA , Friesner RA , Tirado‐Rives J , Jorgensen WL. Evaluation and reparametrization of the OPLS‐AA force field for proteins via comparison with accurate quantum chemical calculations on peptides . J Phys Chem B 2001 ; 105 : 6474 – 6487 .
Gront D , Kmiecik S , Blaszczyk M , Ekonomiuk D , Koliński A. Optimization of protein models . Wires Comput Mol Sci 2012 ; 2 : 479 – 493 .
Zhou H , Zhou Y. Distance‐scaled, finite ideal‐gas reference state improves structure‐derived potentials of mean force for structure selection and stability prediction . Protein Sci 2002 ; 11 : 2714 – 2726 .
Zhu J , Xie L , Honig B. Structural refinement of protein segments containing secondary structure elements: Local sampling, knowledge‐based potentials, and clustering . Proteins 2006 ; 65 : 463 – 479 .
Zhu J , Fan H , Periole X , Honig B , Mark AE. Refining homology models by combining replica‐exchange molecular dynamics and statistical potentials . Proteins 2008 ; 72 : 1171 – 1188 .
Yang Y , Zhou Y. Specific interactions for ab initio folding of protein terminal regions with secondary structures . Proteins 2008 ; 72 : 793 – 803 .
Summa CM , Levitt M. Near‐native structure refinement using in vacuo energy minimization . Proc Natl Acad Sci U S A 2007 ; 104 : 3177 – 3182 .
Samudrala R , Moult J. An all‐atom distance‐dependent conditional probability discriminatory function for protein structure prediction . J Mol Biol 1998 ; 275 : 895 – 916 .
Rodrigues JP , Levitt M Chopra G. KoBaMIN: a knowledge‐based minimization web server for protein structure refinement . Nucleic Acids Res 2012 ; 40 : W323 – W328 .
Kortemme T , Morozov AV , Baker D. An orientation‐dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein‐protein complexes . J Mol Biol 2003 ; 326 : 1239 – 1259 .
Heo L , Park H , Seok C. GalaxyRefine: protein structure refinement driven by side‐chain repacking . Nucleic Acids Res 2013 ; 41 : W384 – 388 .
Jagielska A , Wroblewska L , Skolnick J. Protein model refinement using an optimized physics‐based all‐atom force field . Proc Natl Acad Sci U S A 2008 ; 105 : 8268 – 8273 .
Zhang J , Liang Y , Zhang Y. Atomic‐level protein structure refinement using fragment‐guided molecular dynamics conformation sampling . Structure 2011 ; 19 : 1784 – 1795 .
Nugent T , Cozzetto D , Jones DT. Evaluation of predictions in the CASP10 model refinement category . Proteins 2014 ; 82 ( Suppl 2 ): 98 – 111 .
Krivov GG , Shapovalov MV , Dunbrack RL , Jr. Improved prediction of protein side‐chain conformations with SCWRL4 . Proteins 2009 ; 77 : 778 – 795 .
Bakan A , Meireles LM , Bahar I. ProDy: protein dynamics inferred from theory and experiments . Bioinformatics 2011 ; 27 : 1575 – 1577 .
Tirion MM. Large amplitude elastic motions in proteins from a single‐parameter, atomic analysis . Phys Rev Lett 1996 ; 77 : 1905 – 1908 .
Wallner B , Elofsson A. Pcons5: combining consensus, structural evaluation and fold recognition scores . Bioinformatics 2005 ; 21 : 4248 – 4254 .
Xiang Z , Soto CS , Honig B. Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction . Proc Natl Acad Sci U S A 2002 ; 99 : 7432 – 7437 .
Park H , Lee GR , Heo L , Seok C. Protein loop modeling using a new hybrid energy function and its application to modeling in inaccurate structural environments . PLoS One 2014 ; 9 : e113811
Lee J , Lee D , Park H , Coutsias EA , Seok C. Protein loop modeling by using fragment assembly and analytical loop closure . Proteins 2010 ; 78 : 3428 – 3436 .
Coutsias EA , Seok C , Jacobson MP , Dill KA. A kinematic view of loop closure . J Comput Chem 2004 ; 25 : 510 – 528 .
Lee J , Scheraga HA , Rackovsky S. New optimization method for conformational energy calculations on polypeptides: Conformational space annealing . J Comput Chem 1997 ; 18 : 1222 – 1232 .
Kopp J , Bordoli L , Battey JND , Kiefer F , Schwede T. Assessment of CASP7 predictions for template‐based modeling targets . Proteins 2007 ; 69 : 38 – 56 .
Kryshtafovych A , Monastyrskyy B , Fidelis K. CASP prediction center infrastructure and evaluation measures in CASP10 and CASP ROLL . Proteins 2014 ; 82 ( Suppl 2 ): 7 – 13 .
Chen VB , Arendall WB , III , Headd JJ , Keedy DA , Immormino RM , Kapral GJ , Murray LW , Richardson JS , Richardson DC. MolProbity: all‐atom structure validation for macromolecular crystallography . Acta Crystallogr D Biol Crystallogr 2010 ; 66 : 12 – 21 .
Park H , Seok C. Refinement of unreliable local regions in template‐based protein models . Proteins 2012 ; 80 : 1974 – 1986 .
Park H , Ko J , Joo K , Lee J , Seok C , Lee J. Refinement of protein termini in template‐based modeling using conformational space annealing . Proteins 2011 ; 79 : 2725 – 2734 .
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