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Group: McCammon - library [50 articles]

Nye artikler sendt inn av medlemmer i McCammon -gruppen
  • Local Function Conservation in Sequence and Structure Space
    PLoS Comput Biol, Vol. 4, No. 7. (4 July 2008), e1000105.
    by Nils Weinhold, Oliver Sander, Francisco S Domingues, Thomas Lengauer, Ingolf Sommer
    posted to protein_structure protein_sequence function_prediction by barry to the group McCammon on 2008-09-08 17:53:09 as read along with 2 people and 2 groups cabbagesofdoom Ema structural_bioinformatics Bioinformatics
  • notes A critique of the molecular target-based drug discovery paradigm based on principles of metabolic control: Advantages of pathway-based discovery.
    Metab Eng (20 September 2007)
    by Marc K K Hellerstein
    posted to review drug_design by barry to the group McCammon on 2008-09-06 03:26:44 as *** along with 3 people msierk Ema cmmorel
  • notes Bacterial actin: architecture of the ParMRC plasmid DNA partitioning complex
    The EMBO Journal, Vol. aop, No. current. (24 July 2008)
    by Jeanne Salje, Jan Lowe
    posted to cytoskeleton actin by barry to the group McCammon on 2008-09-06 03:22:22 as **
  • Salt-Mediated Electrostatics in the Association of TATA Binding Proteins to DNA: A Combined Molecular Mechanics/Poisson-Boltzmann Study
    Biophys. J., Vol. 94, No. 12. (15 June 2008), pp. 4634-4645.
    by Johan H Bredenberg, Cristina Russo, Marcia O Fenley
    posted to electrostatics protein_dna solvation by barry to the group McCammon on 2008-08-29 19:08:02 as *** along with 1 person and 2 groups sobolevnrm baker-group structural_bioinformatics
  • Allostery: an illustrated definition for the 'second secret of life'
    Trends in biochemical sciences (13 August 2008)
    by Aron W W Fenton
    posted to allosteric review by barry to the group McCammon on 2008-08-29 19:04:37 as ** along with 1 person and 1 group ruvido structural_bioinformatics
  • notes Rate of Loop Formation in Peptides: A Simulation Study
    Journal of Molecular Biology, Vol. 382, No. 2. (3 October 2008), pp. 556-565.
    by Matthias J Feige, Emanuele Paci
    posted to md_simulation by barry to the group McCammon on 2008-08-29 19:03:07 as ** along with 1 group structural_bioinformatics
  • A B-cell mitogen from a pathogenic trypanosome is a eukaryotic proline racemase
    Nat Med, Vol. 6, No. 8. (2000), pp. 890-897.
    by Bernardo Reina-San-Martin, Wim Degrave, Catherine Rougeot, Alain Cosson, Nathalie Chamond, Anabela Cordeiro-Da-Silva, Mario Arala-Chaves, Antonio Coutinho, Paola Minoprio
    posted to b-cell_mitogen proline racemase trypanosoma_cruzi by cesar to the group McCammon on 2008-08-28 18:11:29 as read
  • Trypanosoma cruzi proline racemases are involved in parasite differentiation and infectivity
    Molecular Microbiology, Vol. 58, No. 1. (October 2005), pp. 46-60.
    by Nathalie Chamond, Maira Goytia, Nicolas Coatnoan, Jean-Christophe Barale, Alain Cosson, Wim M Degrave, Paola Minoprio
    posted to proline_racemases trypanosoma_cruzi by cesar to the group McCammon on 2008-08-28 18:04:01 as **
  • Crystal structure, catalytic mechanism, and mitogenic properties of Trypanosoma cruzi proline racemase.
    Proc Natl Acad Sci U S A (30 January 2006)
    by Alejandro Buschiazzo, Maira Goytia, Francis Schaeffer, Wim Degrave, William Shepard, Christophe Grégoire, Nathalie Chamond, Alain Cosson, Armand Berneman, Nicolas Coatnoan, Pedro M M Alzari, Paola Minoprio
    posted to b-cell_mitogen chagas_disease proline_racemase trypanosoma_cruzi by cesar to the group McCammon on 2008-08-28 18:02:33 as read along with 2 people barry cmmorel
  • Rational Design of Human DNA Ligase Inhibitors that Target Cellular DNA Replication and Repair
    Cancer Res, Vol. 68, No. 9. (1 May 2008), pp. 3169-3177.
    by Xi Chen, Shijun Zhong, Xiao Zhu, Barbara Dziegielewska, Tom Ellenberger, Gerald M Wilson, Alexander D Mackerell, Alan E Tomkinson
    posted to no-tag by iivanov to the group McCammon on 2008-08-27 22:05:27 as ** along with 1 person TOchi
  • Identification and Validation of Human DNA Ligase Inhibitors Using Computer-Aided Drug Design
    J. Med. Chem. (17 July 2008)
    by Shijun Zhong, Xi Chen, Xiao Zhu, Barbara Dziegielewska, Kurtis E Bachman, Tom Ellenberger, Jeff D Ballin, Gerald M Wilson, Alan E Tomkinson, Alexander D Mackerell
    posted to no-tag by iivanov to the group McCammon on 2008-08-27 22:03:46 as ** along with 1 person reyez
  • An Enzymatic Atavist Revealed in Dual Pathways for Water Activation
    PLoS Biology, Vol. 6, No. 8. (1 August 2008), e206.
    by Donghong Min, Helen R Josephine, Hongzhi Li, Clemens Lakner, Iain S Macpherson, Gavin J Naylor, David Swofford, Lizbeth Hedstrom, Wei Yang
    posted to imp_dehydrogenase qm_mm by barry to the group McCammon on 2008-08-26 18:45:20 as ***** along with 2 groups Bioinformatics structural_bioinformatics
  • Membrane proteins: molecular dynamics simulations
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Erik Lindahl, Mark SP Sansom
    posted to coarse_grain ion_channel md_simulation membrane by jmccammon to the group McCammon on 2008-08-21 19:59:02 as ** along with 2 people cat_worth rok
  • Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation
    Current Opinion in Structural Biology, Vol. 17, No. 6. (December 2007), pp. 633-640.
    by Ivet Bahar, Chakra Chennubhotla, Dror Tobi
    posted to coarse_grain md_simulation protein-ligand by jmccammon to the group McCammon on 2008-08-21 19:52:40 as read along with 8 people and 3 groups barry aqeel ruvido cactus sobolevnrm jennifermbui higueruelo LamBras structural_bioinformatics Bioinformatics baker-group
  • Phosphodiester Cleavage in Ribonuclease H Occurs via an Associative Two-Metal-Aided Catalytic Mechanism
    Journal of the American Chemical Society, Vol. 130 (2008), 10955.
    by M De Vivo, Dal, ML Klein
    posted to drug-discovery md_simulation qm-mm by jmccammon to the group McCammon on 2008-08-21 19:37:17 as **
  • Atomistic Insights into Rhodopsin Activation from a Dynamic Model
    Journal of the American Chemical Society, Vol. 130 (2008), 10141.
    by IG Tikhonova, RB Best, S Engel, MC Gershengorn, G Hummer, S Costanzi
    posted to coarse_grain md_simulation by jmccammon to the group McCammon on 2008-08-21 19:28:38 as **
  • Structure of a β1-adrenergic G-protein-coupled receptor
    Nature (25 June 2008)
    by Tony Warne, Maria J Serrano-Vega, Jillian G Baker, Rouslan Moukhametzianov, Patricia C Edwards, Richard Henderson, Andrew GW Leslie, Christopher G Tate, Gebhard FX Schertler
    posted to adrenergic beta1 gpcr membrane by TonyIvetac to the group McCammon on 2008-08-21 18:14:24 as ***** along with 1 person merj
  • Coupling Accelerated Molecular Dynamics Methods with Thermodynamic Integration Simulations
    J. Chem. Theory Comput. (13 August 2008)
    by Cesar A de Oliveira, Donald Hamelberg, JA Mccammon
    posted to accelerated_md free_energy by cesar to the group McCammon on 2008-08-20 22:58:36 as read along with 1 person dmobley
  • Synergistic approach to improve "alchemical" free energy calculation in rugged energy surface.
    The Journal of chemical physics, Vol. 126, No. 14. (14 April 2007)
    by D Min, H Li, G Li, R Bitetti-Putzer, W Yang
    posted to discussion_free_energy free_energy by barry to the group McCammon on 2008-08-20 22:16:00 as ** along with 1 group structural_bioinformatics
  • The Interaction of Phospholipase A2 with a Phospholipid Bilayer: Coarse-Grained Molecular Dynamics Simulations
    Biophys. J. (9 May 2008), biophysj.107.123190.
    by Chze-Ling Wee, Kia Balali-Mood, David Gavaghan, Mark S Sansom
    posted to coarse_grain md_simulation membrane by jmccammon to the group McCammon on 2008-08-20 22:15:41 as *** along with 1 person paulschlesinger
  • REACH Coarse-Grained Biomolecular Simulation: Transferability between Different Protein Structural Classes
    Biophys. J. (9 May 2008), biophysj.108.131714.
    by Kei Moritsugu, Jeremy C Smith
    posted to coarse_grain md_simulation by jmccammon to the group McCammon on 2008-08-20 22:13:18 as *** along with 4 people paulschlesinger choonpeng aqeel rok
  • Hierarchical organization of eglin c native state dynamics is shaped by competing direct and water-mediated interactions
    Proceedings of the National Academy of Sciences, Vol. 105, No. 31. (2008), pp. 10659-10664.
    by Christopher K Materese, Christa C Goldmon, Garegin A Papoian
    posted to md_simulation by jmccammon to the group McCammon on 2008-08-19 23:38:22 as **** along with 1 person OriginalLurch
  • Assessing the performance of implicit solvation models at a nucleic acid surface
    Phys. Chem. Chem. Phys., Vol. 10, No. 32. (2008), pp. 4889-4902.
    by Feng Dong, Jason A Wagoner, Nathan A Baker
    posted to electrostatics solvation by jmccammon to the group McCammon on 2008-08-19 23:13:52 as ****
  • Computational methods for diffusion-influenced biochemical reactions.
    Bioinformatics (30 May 2007)
    by Maciej Dobrzynski, Jordi Vidal Rodríguez, Jaap A A Kaandorp, Joke G G Blom
    posted to brownian_dynamics coarse_grain diffusion by jmccammon to the group McCammon on 2008-08-08 21:33:57 as read along with 3 people jjray balabu dagmar
  • Conservative Algorithm for an Adaptive Change of Resolution in Mixed Atomistic/Coarse-Grained Multiscale Simulations
    Journal of Chemical Theory and Computation (2008)
    by A Heyden, DG Truhlar
    posted to coarse_grain md_simulation by jmccammon to the group McCammon on 2008-08-08 21:30:54 as read
  • Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations
    Journal of Chemical Physics (2008)
    by Y Deng, B Roux
    posted to binding free_energy md_simulation by jmccammon to the group McCammon on 2008-08-08 21:27:43 as read
  • A statistical analysis of the precision of reweighting-based simulations
    Journal of Chemical Physics (2008)
    by T Shen, D Hamelberg
    posted to accelerated_md md_simulation by jmccammon to the group McCammon on 2008-08-08 21:24:37 as read
  • Directionally negative friction: A method for enhanced sampling of rare event kinetics
    Journal of Chemical Physics (2008)
    by J Macfadyen, J Wereszczynski, I Andricioaei
    posted to kinetics langevin_dynamics md_simulation time_correlation_function by jmccammon to the group McCammon on 2008-07-23 01:44:52 as read
  • The importance of stupidity in scientific research
    J Cell Sci, Vol. 121, No. 11. (1 June 2008), 1771.
    by Martin A Schwartz
    posted to advice career essay by barry to the group McCammon on 2008-07-16 22:25:46 as **** along with 5 people and 1 group dullhunk arindrartow ibuch casutton jporternj structural_bioinformatics
  • De Novo Computational Design of Retro-Aldol Enzymes
    Science, Vol. 319, No. 5868. (7 March 2008), pp. 1387-1391.
    by Lin Jiang, Eric A Althoff, Fernando R Clemente, Lindsey Doyle, Daniela Rothlisberger, Alexandre Zanghellini, Jasmine L Gallaher, Jamie L Betker, Fujie Tanaka, Carlos F Barbas, Donald Hilvert, Kendall N Houk, Barry L Stoddard, David Baker
    posted to protein_design protein_ligand structure_refinement by barry to the group McCammon on 2008-07-08 01:28:41 as **** along with 12 people and 2 groups aalibes jwm aprasad dgront zwang sobolevnrm davidlott msuarezdiez scienbox ucbcjbm joseph_x_zhou cambray structural_bioinformatics baker-group
  • Structural flexibility in proteins: impact of the crystal environment
    Bioinformatics, Vol. 24, No. 4. (15 February 2008), pp. 521-528.
    by Konrad Hinsen
    posted to nma by barry to the group McCammon on 2008-07-08 01:28:06 as ** along with 3 people and 1 group sobolevnrm jlh64 scienbox baker-group
  • Protein interactions in human genetic diseases
    Genome Biology, Vol. 9, No. 1. (2008)
    by Benjamin S Bockler, Alex Bateman
    posted to protein-protein review by barry to the group McCammon on 2008-07-08 01:27:26 as read along with 10 people and 1 group balicea frohike neils grahamc aconesa biomcgary barriot mingzhi mclarenv jyuh Bioinformatics
  • Divergent Evolution Within Protein Superfolds Inferred from Profile-based Phylogenetics
    Journal of Molecular Biology, Vol. 354, No. 3. (2 December 2005), pp. 722-737.
    by Douglas L Theobald, Deborah S Wuttke
    posted to phylogeny protein_evolution by barry to the group McCammon on 2008-07-08 01:26:53 as * along with 3 people and 3 groups ana dlr caporaso structural_bioinformatics Bioinformatics biomedical-nlp
  • Protein-protein binding is often associated with changes in protonation state
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Aaron C Mason, Jan H Jensen
    posted to binding protein-protein titration by barry to the group McCammon on 2008-07-08 01:26:01 as ** along with 4 people and 2 groups bicko chad_davis sobolevnrm RamuAnandakrishnan baker-group structural_bioinformatics
  • Allostery: Absence of a Change in Shape Does Not Imply that Allostery Is Not at Play.
    J Mol Biol (29 February 2008)
    by Chung-Jung J Tsai, Antonio Del Sol, Ruth Nussinov
    posted to allosteric review by barry to the group McCammon on 2008-07-08 01:25:18 as *** along with 6 people and 2 groups choonpeng cactus sobolevnrm CameronNeylon higueruelo cchang structural_bioinformatics group
  • Avian influenza virus, a very sticky situation
    Current Opinion in Chemical Biology, Vol. 12, No. 1. (February 2008), pp. 102-108.
    by Mark von Itzstein
    posted to drug_discovery protein_ligand by barry to the group McCammon on 2008-07-08 01:24:41 as ** along with 1 person jmccammon
  • X-ray structure of a prokaryotic pentameric ligand-gated ion channel
    Nature (05 March 2008)
    by Ricarda JC Hilf, Raimund Dutzler
    posted to achr ion_channel by barry to the group McCammon on 2008-07-08 01:24:17 as ** along with 2 people and 1 group neils jmccammon structural_bioinformatics
  • Transition networks for modeling the kinetics of conformational change in macromolecules
    Current Opinion in Structural Biology, Vol. 18, No. 2. (April 2008), pp. 154-162.
    by Frank Noé, Stefan Fischer
    posted to review smd by barry to the group McCammon on 2008-07-08 01:23:34 as *** along with 3 people and 2 groups sobolevnrm paulschlesinger toerst structural_bioinformatics baker-group
  • Association of Aminoglycosidic Antibiotics with the Ribosomal A-Site Studied with Brownian Dynamics
    J. Chem. Theory Comput., Vol. 4, No. 4. (8 April 2008), pp. 549-559.
    by Maciej Długosz, Jan M Antosiewicz, Joanna Trylska
    posted to brownian_dynamics electrostatics by barry to the group McCammon on 2008-07-08 01:22:26 as ** along with 1 person and 1 group sobolevnrm baker-group
  • Accelerated Superposition State Molecular Dynamics for Condensed Phase Systems
    J. Chem. Theory Comput., Vol. 4, No. 4. (8 April 2008), pp. 560-568.
    by Michele Ceotto, Gary S Ayton, Gregory A Voth
    posted to accelerated_md md_simulation by barry to the group McCammon on 2008-07-08 01:21:07 as **
  • How Efficient Is Replica Exchange Molecular Dynamics? An Analytic Approach
    J. Chem. Theory Comput., Vol. 4, No. 4. (8 April 2008), pp. 626-636.
    by Hugh Nymeyer
    posted to md_simulation replica_exchange by barry to the group McCammon on 2008-07-08 01:17:17 as ** along with 3 people and 2 groups agrossfield sobolevnrm loison baker-group structural_bioinformatics
  • Protonation free energy levels in complex molecular systems
    Biopolymers, Vol. 9999, No. 9999. (2007), NA.
    by Jan M Antosiewicz
    posted to electrostatics titration by barry to the group McCammon on 2008-07-08 01:15:32 as ** along with 1 person and 1 group sobolevnrm baker-group
  • Novel Method for Probing the Specificity Binding Profile of Ligands: Applications to HIV Protease
    Chemical Biology & Drug Design, Vol. 71, No. 5. (2008), pp. 387-407.
    by Woody Sherman, Bruce Tidor
    posted to drug_discovery protein_ligand by barry to the group McCammon on 2008-07-08 01:14:49 as ** along with 1 person and 1 group jmccammon structural_bioinformatics
  • Calculation of protein-ligand binding free energy by using a polarizable potential
    Proceedings of the National Academy of Sciences, Vol. 105, No. 17. (29 April 2008), pp. 6290-6295.
    by Dian Jiao, Pavel A Golubkov, Thomas A Darden, Pengyu Ren
    posted to binding free_energy md_simulation protein-ligand by barry to the group McCammon on 2008-07-08 01:12:03 as ** along with 3 people and 2 groups jmccammon biehl sobolevnrm baker-group structural_bioinformatics
  • From the Cover: A dry ligand-binding cavity in a solvated protein
    Proceedings of the National Academy of Sciences, Vol. 105, No. 17. (29 April 2008), pp. 6296-6301.
    by Johan Qvist, Monika Davidovic, Donald Hamelberg, Bertil Halle
    posted to free_energy md_simulation protein-ligand solvation by barry to the group McCammon on 2008-07-08 01:11:30 as ** along with 2 people and 2 groups jmccammon sobolevnrm structural_bioinformatics baker-group
  • Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution
    Science, Vol. 320, No. 5882. (13 June 2008), pp. 1471-1475.
    by Oliver F Lange, Nils-Alexander Lakomek, Christophe Fares, Gunnar F Schroder, Korvin F Walter, Stefan Becker, Jens Meiler, Helmut Grubmuller, Christian Griesinger, Bert L de Groot
    posted to binding protein-protein by barry to the group McCammon on 2008-07-08 00:52:29 as ** along with 4 people and 2 groups paulschlesinger higueruelo jmccammon cchang structural_bioinformatics group
  • The Poisson-Boltzmann model for tRNA: Assessment of the calculation set-up and ionic concentration cutoff
    Journal of Computational Chemistry, Vol. 29, No. 12. (2008), pp. 1970-1981.
    by Magdalena Gruziel, Pawel Grochowski, Joanna Trylska
    posted to electrostatics by barry to the group McCammon on 2008-07-08 00:51:34 as ** along with 1 person and 1 group RamuAnandakrishnan structural_bioinformatics
  • Protein model refinement using an optimized physics-based all-atom force field
    Proceedings of the National Academy of Sciences, Vol. 105, No. 24. (17 June 2008), pp. 8268-8273.
    by Anna Jagielska, Liliana Wroblewska, Jeffrey Skolnick
    posted to coarse_grain replica_exchange by barry to the group McCammon on 2008-07-08 00:49:57 as ** along with 3 people and 1 group RamuAnandakrishnan jmccammon zwang structural_bioinformatics
  • Pathway and Endpoint Free Energy Calculations for Cyclic Nucleotide Binding to HCN Channels
    Biophys. J., Vol. 94, No. 12. (15 June 2008), pp. L90-92.
    by Lei Zhou, Steven A Siegelbaum
    posted to binding electrostatics free_energy md_simulation protein-ligand by barry to the group McCammon on 2008-07-08 00:49:17 as ** along with 1 person jmccammon
  • Stochastic Binding of Ca2+ Ions in the Dyadic Cleft; Continuous versus Random Walk Description of Diffusion
    Biophys. J., Vol. 94, No. 11. (1 June 2008), pp. 4184-4201.
    by Johan Hake, Glenn T Lines
    posted to binding brownian_dynamics ion_channel by barry to the group McCammon on 2008-07-08 00:47:05 as ** along with 1 person jmccammon
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