ibuch's library 91 articles Export

	Simultaneous prediction of protein folding and docking at high resolution [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 45. (10 November 2009), pp. 18978-18983. by Rhiju Das, Ingemar AndrÃ©, Yang Shen, et al.Yibing Wu, Alexander Lemak, Sonal Bansal, Cheryl H. Arrowsmith, Thomas Szyperski, David Baker posted to folding docking by ibuch on 2009-11-11 10:53:16 as along with 1 person zwang
	A noncatalytic domain conserved among cytoplasmic protein-tyrosine kinases modifies the kinase function and transforming activity of Fujinami sarcoma virus P130gag-fps. [My Copy] Molecular and cellular biology, Vol. 6, No. 12. (December 1986), pp. 4396-4408. by I. Sadowski, J. C. Stone, T. Pawson posted to sh2 by ibuch on 2009-11-10 14:04:43 as
	High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations [My Copy] PLoS Comput Biol, Vol. 5, No. 10. (9 October 2009), e1000528. by Noriaki Okimoto, Noriyuki Futatsugi, Hideyoshi Fuji, et al.Atsushi Suenaga, Gentaro Morimoto, Ryoko Yanai, Yousuke Ohno, Tetsu Narumi, Makoto Taiji posted to md highthroughput docking bindingaffinities by ibuch on 2009-11-05 09:26:58 as along with 5 people and 1 group klexa skywalkerus02 kentsis reyez barry McCammon
	Refinement of homology-based protein structures by molecular dynamics simulation techniques. [My Copy] Protein science : a publication of the Protein Society, Vol. 13, No. 1. (January 2004), pp. 211-220. by Hao Fan, Alan E. Mark posted to structurerefinement by ibuch on 2009-10-26 14:28:22 as
	Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8 [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 77, No. S9. (2009), pp. 114-122. by Elmar Krieger, Keehyoung Joo, Jinwoo Lee, et al.Jooyoung Lee, Srivatsan Raman, James Thompson, Mike Tyka, David Baker, Kevin Karplus posted to structurerefinement by ibuch on 2009-10-26 14:27:22 as along with 1 person reyez
	Epitope mapping of a bactericidal monoclonal antibody against the factor H binding protein of Neisseria meningitidis. [My Copy] Journal of molecular biology, Vol. 386, No. 1. (13 February 2009), pp. 97-108. by Maria Scarselli, Francesca Cantini, Laura Santini, et al.Daniele Veggi, Sara Dragonetti, Claudio Donati, Silvana Savino, Marzia M. Giuliani, Maurizio Comanducci, Federica Di Marcello, Giacomo Romagnoli, Mariagrazia Pizza, Lucia Banci, Rino Rappuoli posted to reversevaccinology epitopemapping by ibuch on 2009-10-20 11:40:36 as
	Post-genomic vaccine development. [My Copy] FEBS letters, Vol. 580, No. 12. (22 May 2006), pp. 2985-2992. by Davide Serruto, Rino Rappuoli posted to reversevaccinology by ibuch on 2009-10-20 11:39:40 as
	Coarse-Grained MD Simulations and Protein−Protein Interactions: The Cohesin−Dockerin System [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 9. (8 September 2009), pp. 2465-2471. by Benjamin A. Hall, Mark S. P. Sansom posted to interaction cg by ibuch on 2009-09-23 14:59:11 as along with 2 people and 1 group A_Coletta_Thesis qshao Structural Biology Group TorVergata
	Toll-like receptors in innate immunity. [My Copy] Int Immunol, Vol. 17, No. 1. (January 2005), pp. 1-14. by K. Takeda, S. Akira posted to innateimmunity tlr tlr4 by ibuch on 2009-07-14 09:33:26 as along with 1 person jen_drake
	Binding of Small-Molecule Ligands to Proteins: What You See Is Not Always What You Get [My Copy] Vol. 17, No. 4. (15 April 2009), pp. 489-498. by David L. Mobley, Ken A. Dill posted to binding proteinligand by ibuch on 2009-07-14 09:25:53 as along with 2 people and 1 group nanonan barry McCammon
	Kinetic and binding effects in peptide substrate selectivity of matrix metalloproteinase-2: Molecular dynamics and QM/MM calculations [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2009), NA. by Natalia Díaz, Dimas Suárez, Ernesto Suárez posted to binding free-energy proteinligand by ibuch on 2009-07-13 15:56:09 as
	ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 6. (9 June 2009), pp. 1632-1639. by M. J. Harvey, G. Giupponi, G. De Fabritiis posted to acemd hpc md by ibuch on 2009-07-08 14:55:25 as along with 4 people and 1 group qshao jmccammon r2s2 mmuecke McCammon
	How to write consistently boring scientific literature [My Copy] Oikos, Vol. 116, No. 5. (May 2007), pp. 723-727. by Kaj Sand-Jensen posted to advice writing by ibuch on 2009-07-07 17:41:44 as along with 189 people and 14 groups jmzhuo Horduna toszko chriswillmott mthomure Thaverkamp ibre sfalsharif lafuente Sergey_gerbek Torsten_Holmer aaltenburger tminze mmborges Dannycoutinho soniapereira Anita13 simonhearne rudalert ulrichs duel_jetty nmsx TVB timsenior livingthingdan alhoori poojamaj letillett christianholz amynmoore pvdg leonardo cgravlee bhengeveld ansobol jrw proportional wendygarnica jsatkosk eumelus pdpcosta AnthonySoprano wasteland93 buchgeher lmichan NIlz sxs732 artaban421 kieranhood rabit pauljhurtado SantoshKalwar aldra zchen75 nbawia Zephyrus jgebbie lanmuzi amadeusstevenson akuhn metatheory Fneesen hkimura beete CamilleH luciensamary jcreed R_C_Cordeiro thenose cyounkin robertlischke bspackman lyss sebpaquet c_hughes klauso kaiserm tomhebbron tarokiritani nGrenier girabbit jaia CulCog alexander_bauer Gaetan cjhall mdwelsh231 sniklas polivares MurphysLab ckai1 tux2000 petko_bogdanov carelcad Tomste yangjustinc thegoose michaelbanks mrt2k9 marekrud pawelsobko klexa tunheim Elley AJCann amoreno operon barry jod999 guhjy pick600 leliavski ombamawu mjoach Publicase Thermaneutist gwallau tnhh signori birte bertelsen mmuecke Mohan-S Dori2008 konstantinos charoy flips arsyed sjefarrar rohanlowe syah jjray zzh1986 brownstudy abellogin fungal sgeuter jkglenn psique anphony ajaymalik jjrohal markusd conradlee mschmer gkoenig natstreet cisevol silberbauer ArtemPankin druvus allysonlister dullhunk VGreiff dbk ultrascichick ahaeusler rickl brian toomash orca Borelli cmunson lfriedl sterovetta maike echinotrix awooga yEvb0 scpeters jford pratap williamdwalker sjones pseudopharm cjeans sensesublime TaqSys soumitri GeeSharpMinor tumo rebeccamancy ascharle suizan kaniko erklaerbaer boosda hejibo randomname UWA Science Communication Med Anthro @ UF Scholarly Communication McCammon BergmanLab Khavkin's lab kdl Neuroscience STS ColDyn feminist_technoscience OrganizationResearch Enactment Academic Writing, Literacies and Discourse
	Protein Dynamism and Evolvability [My Copy] Science, Vol. 324, No. 5924. (10 April 2009), pp. 203-207. by Nobuhiko Tokuriki, Dan S. Tawfik posted to md by ibuch on 2009-07-07 17:35:57 as along with 18 people and 3 groups anuragsethi ahmetbakan kevinchannon klexa lauresultan dbikard ramiro2k barry pablocarb ramanuja sobolevnrm biomcgary hsekiguc VGreiff phoenixzxl zwang jdoconnell paulschlesinger structural_bioinformatics McCammon baker-group
	TLR4 polymorphisms and ageing: implications for the pathophysiology of age-related diseases. [My Copy] Journal of clinical immunology, Vol. 29, No. 4. (July 2009), pp. 406-415. by C. R. Balistreri, G. Colonna-Romano, D. Lio, G. Candore, C. Caruso posted to ageing alzheimer tlr4 by ibuch on 2009-07-07 17:29:20 as
	Dietary factors lead to innate immune activation in asthma. [My Copy] Pharmacology & therapeutics, Vol. 123, No. 1. (15 July 2009), pp. 37-53. by L. G. Wood, P. G. Gibson posted to asthma tlr4 by ibuch on 2009-07-07 17:27:25 as along with 1 person and 1 group HEIRS HEIRS - Environmental Illness Research
	The structural basis of lipopolysaccharide recognition by the TLR4-MD-2 complex. [My Copy] Nature, Vol. 458, No. 7242. (30 April 2009), pp. 1191-1195. by B. S. Park, D. H. Song, H. M. Kim, B. S. Choi, H. Lee, J. O. Lee posted to tlr4 by ibuch on 2009-07-07 16:41:21 as
	Essential Roles of Hydrophobic Residues in Both MD-2 and Toll-like Receptor 4 in Activation by Endotoxin [My Copy] J. Biol. Chem., Vol. 284, No. 22. (29 May 2009), pp. 15052-15060. by Nusa Resman, Jozica Vasl, Alja Oblak, et al.Primoz Pristovsek, Theresa L. Gioannini, Jerrold P. Weiss, Roman Jerala posted to tlr4 by ibuch on 2009-07-07 15:49:18 as
	Targeting innate immunity protein kinase signalling in inflammation. [My Copy] Nature reviews. Drug discovery, Vol. 8, No. 6. (June 2009), pp. 480-499. by Matthias Gaestel, Alexey Kotlyarov, Michael Kracht posted to drugtargets innateimmunity kinases by ibuch on 2009-07-02 16:19:24 as along with 2 people guhjy renatomilani
	Lambda-dynamics free energy simulation methods. [My Copy] Journal of computational chemistry, Vol. 30, No. 11. (August 2009), pp. 1692-1700. by J. L. Knight, C. L. Brooks posted to free-energy lambdadynamics methods by ibuch on 2009-07-02 13:32:04 as along with 3 people and 1 group klexa agrossfield sobolevnrm baker-group
	Finite Size Effects in Simulations of Protein Aggregation [My Copy] PLoS ONE, Vol. 3, No. 7. (9 July 2008), e2641. by Amol Pawar, Giorgio Favrin posted to aggregation finitesize by ibuch on 2009-07-01 15:53:27 as
	Three-/four-repeat-dependent aggregation profile of tau microtubule-binding domain clarified by dynamic light scattering analysis [My Copy] Biochemical and Biophysical Research Communications, Vol. 385, No. 2. (24 July 2009), pp. 236-240. by Etsuko Sugino, Chisato Nishiura, Katsuhiko Minoura, et al.Yasuko In, Miho Sumida, Taizo Taniguchi, Koji Tomoo, Toshimasa Ishida posted to aggregation tau by ibuch on 2009-07-01 15:33:31 as
	Structural and Thermodynamic Basis for the Interaction of the Src SH2 Domain with the Activated Form of the PDGF β-receptor [My Copy] Journal of Molecular Biology, Vol. 328, No. 3. (02 May 2003), pp. 655-668. by Olga Y. Lubman, Gabriel Waksman posted to binding proteinligand sh2 by ibuch on 2009-05-28 17:48:08 as
	Inclusion of ionization states of ligands in affinity calculations [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 76, No. 1. (2009), pp. 138-150. by Serena Donnini, Alessandra Villa, Gerrit Groenhof, Alan E. Mark, Rik K. Wierenga, André H. Juffer posted to free-energy ionization proteinligand by ibuch on 2009-05-15 11:06:23 as along with 5 people and 2 groups flbarroso onufriev rbaron sobolevnrm RamuAnandakrishnan McCammon baker-group
	Comparison of simple potential functions for simulating liquid water [My Copy] The Journal of Chemical Physics, Vol. 79, No. 2. (1983), pp. 926-935. by William L. Jorgensen, Jayaraman Chandrasekhar, Jeffry D. Madura, Roger W. Impey, Michael L. Klein posted to no-tag by ibuch on 2009-05-08 11:31:00 as along with 17 people and 1 group jmparks fralium bmduggan kulinskii Lombardo_7 paddydu dfgreen softsimu mleis ttjoseph ffranca easybakemuffin ashaytan RamuAnandakrishnan r2s2 pavanghatty Diego_Prada CMB
	Standard Free Energy of Binding from a One-Dimensional Potential of Mean Force [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 4. (March 2009), pp. 909-918. by Slimane Doudou, Neil A. Burton, Richard H. Henchman posted to md methods mscproject proteinligand umbrellasampling by ibuch on 2009-04-17 21:09:58 as along with 4 people and 3 groups jmccammon A_Coletta_Thesis carlosjavierna sobolevnrm McCammon Structural Biology Group TorVergata baker-group
	Multidimensional free-energy calculations using the weighted histogram analysis method [My Copy] Journal of Computational Chemistry, Vol. 16, No. 11. (1995), pp. 1339-1350. by Shankar Kumar, John M. Rosenberg, Djamal Bouzida, Robert H. Swendsen, Peter A. Kollman posted to md methods mscproject umbrellasampling wham by ibuch on 2009-04-17 20:56:52 as along with 2 people and 1 group A_Coletta_Thesis dgront Structural Biology Group TorVergata
	Insights from the energetics of water binding at the domain-ligand interface of the Src SH2 domain. [My Copy] Proteins, Vol. 72, No. 4. (September 2008), pp. 1290-1297. by G. De Fabritiis, S. Geroult, P. V. Coveney, G. Waksman posted to md mscproject proteinligand sh2 by ibuch on 2009-04-17 19:49:30 as
	Mechanism of coupled folding and binding of an intrinsically disordered protein [My Copy] Nature, Vol. 447, No. 7147. (23 May 2007), pp. 1021-1025. by Kenji Sugase, H. Jane Dyson, Peter E. Wright posted to binding folding iup by ibuch on 2009-04-17 15:41:39 as along with 8 people chemrahul82 ubcg08l jteyra cjeans allmensch amwands hsekiguc cactus
	Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model [My Copy] Journal of Chemical Theory and Computation, Vol. 0, No. 0. (0000) by Devleena Shivakumar, Yuqing Deng, Benoît Roux posted to binding highthroughput mscproject proteinligand by ibuch on 2009-03-30 13:59:02 as along with 3 people and 1 group carlosjavierna pmk sobolevnrm baker-group
	Heterodimer formation of wild-type and amyotrophic lateral sclerosis-causing mutant Cu/Zn-Superoxide dismutase induces toxicity independent of protein aggregation. [My Copy] Hum Mol Genet (2008) by H. Witan, A. Kern, I. Koziollek-Drechsler, R. Wade, C. Behl, A. M. Clement posted to aggregation dimerization sod by ibuch on 2009-03-29 19:19:02 as along with 2 people and 1 group thegoose2 tharris C. elegans / WormBase
	Amyloid-dependent triosephosphate isomerase nitrotyrosination induces glycation and tau fibrillation [My Copy] Brain (27 February 2009), awp023. by Francesc X. Guix, Gerard Ill-Raga, Ramona Bravo, et al.Tadashi Nakaya, Gianni de Fabritiis, Mireia Coma, Gian P. Miscione, Jordi Villa-Freixa, Toshiharu Suzuki, Xavier Fernandez-Busquets, Miguel A. Valverde, Bart de Strooper, Francisco J. Munoz posted to tpi tau aggregation by ibuch on 2009-03-26 11:24:28 as
	Escaping free-energy minima. [My Copy] Proc Natl Acad Sci U S A, Vol. 99, No. 20. (1 October 2002), pp. 12562-12566. by A. Laio, M. Parrinello posted to md metadynamics methods by ibuch on 2009-02-12 13:26:49 as along with 6 people and 1 group howerja apaydin baaden and_ped10 Diego_Prada AndreaColetta Jiang Research Group
	Computations of Standard Binding Free Energies with Molecular Dynamics Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 8. (26 January 2009), pp. 2234-2246. by Yuqing Deng, Benoît Roux posted to binding free-energy mscproject by ibuch on 2009-01-30 11:13:20 as along with 9 people and 2 groups anuragsethi flbarroso mikaellund sobolevnrm barry jmccammon willard agrossfield carlosjavierna baker-group McCammon
	Binding specificity of SH2 domains: insight from free energy simulations. [My Copy] Proteins, Vol. 74, No. 4. (2 March 2009), pp. 996-1007. by Wenxun Gan, Benoît Roux posted to binding mscproject sh2 by ibuch on 2009-01-30 11:12:22 as along with 2 people and 1 group allmensch jmccammon McCammon
	Interactions between amides in solution and the thermodynamics of weak binding [My Copy] Journal of the American Chemical Society, Vol. 111, No. 10. (1 May 1989), pp. 3770-3771. by William L. Jorgensen posted to binding mscproject by ibuch on 2009-01-30 11:11:06 as
	High-throughput calculation of protein-ligand binding affinities: modification and adaptation of the MM-PBSA protocol to enterprise grid computing. [My Copy] Journal of chemical information and modeling, Vol. 46, No. 3. (n 2006), pp. 999-1005. by S. P. Brown, S. W. Muchmore posted to binding grid proteinligand by ibuch on 2008-12-29 16:37:28 as
	Calculation of absolute protein-ligand binding free energy using distributed replica sampling [My Copy] The Journal of Chemical Physics, Vol. 129, No. 15. (2008) by Tomas Rodinger, Lynne P. Howell, Régis Pomès posted to binding md methods mscproject proteinligand by ibuch on 2008-11-24 16:12:51 as along with 3 people and 2 groups arlam jmccammon yzlab Chang group McCammon
	The Misused Impact Factor [My Copy] Science, Vol. 322, No. 5899. (10 October 2008), 165. by Kai Simons posted to impactfactor publishing by ibuch on 2008-10-10 14:20:47 as along with 10 people and 3 groups lbjay willwade lesikv applebyb jago Zephyrus leonardo yuhc dullhunk barry Convention on Knowledge Commons Roswell Cancer Crosstalk McCammon
	The impact of accelerator processors for high-throughput molecular modeling and simulation [My Copy] Drug Discovery Today, Vol. 13, No. 23-24. (16 December 2008), pp. 1052-1058. by G. Giupponi, M. Harvey, G. Defabritiis posted to gpu grid hpc md mscproject by ibuch on 2008-09-25 11:55:11 as along with 1 person lavinp
	Hydra: A Self Regenerating High Performance Computing Grid for Drug Discovery [My Copy] J. Chem. Inf. Model. (14 March 2008) by Drew Bullard, Alberto Gobbi, Matthew A. Lardy, Charles Perkins, Zach Little posted to drugdiscovery grid hpc mscproject by ibuch on 2008-09-25 11:45:00 as along with 2 people mrt2k9 middledomain
	Automated Molecular Simulation Based Binding Affinity Calculator for Ligand-Bound HIV-1 Proteases. [My Copy] Journal of chemical information and modeling (19 August 2008) by S K. Sadiq, David Wright, Simon J. Watson, Stefan J. Zasada, Ileana Stoica, Peter V. Coveney posted to hiv hpc md mscproject proteinligand by ibuch on 2008-09-25 11:43:02 as along with 2 people and 1 group mijogiffin skoddet Nielsen group
	Design of a grid service-based platform for in silico protein-ligand screenings. [My Copy] Computer methods and programs in biomedicine (2 September 2008) by Marshall J J. Levesque, Kohei Ichikawa, Susumu Date, Jason H H. Haga posted to drugdiscovery grid md mscproject proteinligand by ibuch on 2008-09-25 11:03:24 as
	The importance of stupidity in scientific research [My Copy] J Cell Sci, Vol. 121, No. 11. (1 June 2008), 1771. by Martin A. Schwartz posted to advice research science by ibuch on 2008-08-09 10:54:04 as along with 36 people and 2 groups tomhebbron Sergey_gerbek sarelfa DLLP mmborges CarlosMorais Anita13 soniapereira vigneshjvn munzmarci CulCog jxl mutesa brembs operon yangjustinc coela silberbauer eyliu Publicase Thermaneutist spl michaelbanks bayesian alexgeorgiou chemistmd susz idoerg sriesenfeld cerca aramata dullhunk arindrartow barry casutton jporternj McCammon structural_bioinformatics
	Knowledge environments representing molecular entities for the virtual physiological human. [My Copy] Philosophical transactions. Series A, Mathematical, physical, and engineering sciences, Vol. 366, No. 1878. (13 September 2008), pp. 3091-3110. by Martin Hofmann-Apitius, Juliane Fluck, Laura Furlong, et al.Oriol Fornes, Corinna Kolářik, Susanne Hanser, Martin Boeker, Stefan Schulz, Ferran Sanz, Roman Klinger, Theo Mevissen, Tobias Gattermayer, Baldo Oliva, Christoph M M. Friedrich posted to knowledgemanagement vph by ibuch on 2008-08-06 15:53:10 as along with 3 people fgibson dullhunk guhjy
	Scalable molecular dynamics with NAMD [My Copy] Journal of Computational Chemistry, Vol. 26, No. 16. (December 2005), pp. 1781-1802. by James C. Phillips, Rosemary Braun, Wei Wang, et al.James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kalé, Klaus Schulten posted to md mscproject namd by ibuch on 2008-07-31 10:46:44 as along with 19 people and 5 groups pjkiley flbarroso yxue r2s2 grondina rpetrenko oteri oceanwind dfgreen vahmurk gisle dimka jwm ttjoseph sangeetha yoel_rf bilab wilsoros sobolevnrm Radiation_Damage Stressosome Bioinformatics insilicodrug baker-group
	The calculation of the potential of mean force using computer simulations [My Copy] Computer Physics Communications, Vol. 91, No. 1-3. (2 September 1995), pp. 275-282. by Benoit Roux posted to md mscproject pmf by ibuch on 2008-07-28 15:21:57 as along with 2 people stephenbond ashaytan
	Calculation of absolute protein-ligand binding free energy from computer simulations. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 19. (10 May 2005), pp. 6825-6830. by H. J. Woo, B. Roux posted to binding md mscproject by ibuch on 2008-07-28 14:35:15 as along with 4 people flbarroso LamBras ttjoseph ashaytan
	Energetics of ion conduction through the gramicidin channel. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, No. 1. (6 January 2004), pp. 117-122. by T. W. Allen, O. S. Andersen, B. Roux posted to ionchannel md mscproject by ibuch on 2008-07-25 16:39:06 as along with 1 person ruvido
	Molecular dynamics -- potential of mean force calculations as a tool for understanding ion permeation and selectivity in narrow channels [My Copy] Biophysical Chemistry In Ion Hydration Special Issue, Vol. 124, No. 3. (1 December 2006), pp. 251-267. by Toby W. Allen, Olaf S. Andersen, Benoit Roux posted to ionchannel md mscproject by ibuch on 2008-07-25 16:38:34 as along with 2 people and 3 groups barry sobolevnrm structural_bioinformatics Bioinformatics baker-group

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ibuch's library 91 articles Export

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