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Group: McCammon - library [73 articles]

Neue Artikel von Mitliedern der Gruppe McCammon Gruppe
  • Mapping a molecular link between allosteric inhibition and activation of the glycine receptor
    Nat Struct Mol Biol, Vol. 15, No. 10. (October 2008), pp. 1084-1093.
    by Paul S Miller, Maya Topf, Trevor G Smart
    posted to loop cys by abebe to the group McCammon on 2008-10-06 18:21:14 as **
  • Structural model for strain-dependent microtubule activation of Mg-ADP release from kinesin
    Nat Struct Mol Biol, Vol. 15, No. 10. (October 2008), pp. 1067-1075.
    by Ryo Nitta, Yasushi Okada, Nobutaka Hirokawa
    posted to kinesin by abebe to the group McCammon on 2008-10-06 18:14:53 as *** along with 1 person barry
  • Crystal structure of an extensively simplified variant of bovine pancreatic trypsin inhibitor in which over one-third of the residues are alanines.
    Proceedings of the National Academy of Sciences of the United States of America (30 September 2008)
    by Mohammad Monirul M Islam, Shihori Sohya, Keiichi Noguchi, Masafumi Yohda, Yutaka Kuroda
    posted to protein_structure protein_design bpti by barry to the group McCammon on 2008-10-05 19:12:36 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • A minimalist network model for coarse-grained normal mode analysis and its application to biomolecular x-ray crystallography.
    Proceedings of the National Academy of Sciences of the United States of America (1 October 2008)
    by Mingyang Lu, Jianpeng Ma
    posted to nma coarse_grain by barry to the group McCammon on 2008-10-05 19:05:40 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • Evaluation of an inverse molecular design algorithm in a model binding site
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by David J Huggins, Michael D Altman, Bruce Tidor
    posted to docking by barry to the group McCammon on 2008-10-05 18:59:32 as * along with 1 person and 1 group middledomain structural_bioinformatics
  • Protein co-evolution, co-adaptation and interactions
    The EMBO Journal, Vol. aop, No. current. (25 September 2008)
    by Florencio Pazos, Alfonso Valencia
    posted to review protein_protein phylogeny correlated_mutations by barry to the group McCammon on 2008-10-02 20:24:17 as ***** along with 1 person and 2 groups sjcockell structural_bioinformatics Bioinformatics
  • Flexible ligand docking to multiple receptor conformations: a practical alternative.
    Current opinion in structural biology, Vol. 18, No. 2. (April 2008), pp. 178-184.
    by M Totrov, R Abagyan
    posted to review md_simulation docking by barry to the group McCammon on 2008-10-02 19:48:14 as ** along with 1 person and 2 groups aqeel structural_bioinformatics Bioinformatics
  • The structure of protein evolution and the evolution of protein structure
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Richard A Goldstein
    posted to review protein_structure protein_evolution fold_space by barry to the group McCammon on 2008-10-02 19:46:30 as ** along with 3 people and 2 groups bpb zwang cmzmasek structural_bioinformatics Bioinformatics
  • notes Understanding mechanisms governing protein-protein interactions from synthetic binding interfaces
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Anthony A Kossiakoff, Shohei Koide
    posted to review protein_protein protein_dynamics by barry to the group McCammon on 2008-10-02 19:21:01 as ** along with 1 person and 2 groups paulschlesinger structural_bioinformatics Bioinformatics
  • A Specificity Map for the PDZ Domain Family
    PLoS Biology, Vol. 6, No. 9. (1 September 2008), e239.
    by Raffi Tonikian, Yingnan Zhang, Stephen L Sazinsky, Bridget Currell, Jung-Hua Yeh, Boris Reva, Heike A Held, Brent A Appleton, Marie Evangelista, Yan Wu, Xiaofeng Xin, Andrew C Chan, Somasekar Seshagiri, Laurence A Lasky, Chris Sander, Charles Boone, Gary D Bader, Sachdev S Sidhu
    posted to protein_protein pdz by barry to the group McCammon on 2008-09-30 18:44:35 as *** along with 1 person and 2 groups cabbagesofdoom structural_bioinformatics Bioinformatics
  • notes An Inhibitor of FtsZ with Potent and Selective Anti-Staphylococcal Activity
    Science, Vol. 321, No. 5896. (19 September 2008), pp. 1673-1675.
    by David J Haydon, Neil R Stokes, Rebecca Ure, Greta Galbraith, James M Bennett, David R Brown, Patrick J Baker, Vladimir V Barynin, David W Rice, Sveta E Sedelnikova, Jonathan R Heal, Joseph M Sheridan, Sachin T Aiwale, Pramod K Chauhan, Anil Srivastava, Amit Taneja, Ian Collins, Jeff Errington, Lloyd G Czaplewski
    posted to tubulin ftsz drug_design cytoskeleton by barry to the group McCammon on 2008-09-29 01:52:45 as read along with 1 person and 2 groups madhadron structural_bioinformatics Bioinformatics
  • Intrinsic Free Energy of the Conformational Transition of the KcsA Signature Peptide from Conducting to Nonconducting State
    J. Chem. Theory Comput., Vol. 4 (13 August 2008), pp. 1541-1554.
    by Ilja V Khavrutskii, Mikolai Fajer, JA Mccammon
    posted to md_simulation ion_channel free_energy by jmccammon to the group McCammon on 2008-09-28 00:04:07 as read along with 1 person dmobley
  • Coupling Accelerated Molecular Dynamics Methods with Thermodynamic Integration Simulations
    J. Chem. Theory Comput., Vol. 4 (13 August 2008), 1516-1525.
    by CAF de Oliveira, D Hamelberg, JA Mccammon
    posted to md_simulation free_energy accelerated_md by jmccammon to the group McCammon on 2008-09-27 23:51:04 as read along with 2 people dmobley cesar
  • Automated clustering of probe molecules from solvent mapping of protein surfaces: new algorithms applied to hot-spot mapping and structure-based drug design.
    Journal of computer-aided molecular design (5 August 2008)
    by Michael G Lerner, Kristin L Meagher, Heather A Carlson
    posted to protein-ligand drug-discovery by jmccammon to the group McCammon on 2008-09-27 20:37:40 as ** along with 2 people sschurer higueruelo
  • An improved relaxed complex scheme for receptor flexibility in computer-aided drug design.
    J Comput Aided Mol Des (15 January 2008)
    by Rommie E Amaro, Riccardo Baron, J A McCammon
    posted to protein-ligand md_simulation drug-discovery by jmccammon to the group McCammon on 2008-09-27 20:31:32 as read along with 4 people rbaron higueruelo kazemi LamBras
  • Molecular modeling on pyruvate phosphate dikinase of Entamoeba histolytica and in silico virtual screening for novel inhibitors
    Journal of Computer-Aided Molecular Design, Vol. 22, No. 9. (2008), pp. 647-660.
    by Preyesh Stephen, Ramachandran Vijayan, Audesh Bhat, N Subbarao, R Bamezai
    posted to protein-ligand drug-discovery by jmccammon to the group McCammon on 2008-09-27 20:21:34 as **
  • Reconstructing atomistic detail for coarse-grained models with resolution exchange
    Journal of Chemical Physics (2008)
    by P Liu, Q Shi, E Lyman, GA Voth
    posted to replica_exchange monte_carlo coarse_grain by jmccammon to the group McCammon on 2008-09-27 20:01:44 as **
  • CHARMMing: A New, Flexible Web Portal for CHARMM
    J. Chem. Inf. Model. (13 August 2008)
    by Benjamin T Miller, Rishi P Singh, Jeffery B Klauda, Milan Hodošček, Bernard R Brooks, Lee H Woodcock
    posted to md_simulation drug-discovery by jmccammon to the group McCammon on 2008-09-27 19:30:35 as ** along with 2 people middledomain reyez
  • From coarse-grain to all-atom: Toward multiscale analysis of protein landscapes
    Proteins: Structure, Function, and Bioinformatics, Vol. 68, No. 3. (2007), pp. 646-661.
    by Allison P Heath, Lydia E Kavraki, Cecilia Clementi
    posted to protein_structure coarse_grain by barry to the group McCammon on 2008-09-26 18:14:38 as *** along with 2 people and 2 groups aqeel mijam structural_bioinformatics Bioinformatics
  • Enzymes with lid-gated active sites must operate by an induced fit mechanism instead of conformational selection.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 105, No. 37. (16 September 2008), pp. 13829-13834.
    by SM Sullivan, T Holyoak
    posted to no-tag by TonyIvetac to the group McCammon on 2008-09-23 20:44:21 as *** along with 1 person and 1 group barry structural_bioinformatics
  • The ionic environment determines ribozyme cleavage rate by modulation of nucleobase pK a -- Smith et al. 14 (9): 1942 -- RNA
    posted to nucleic_acids electrostatics by jmccammon to the group McCammon on 2008-09-12 18:21:18 as ** along with 1 person blu
  • Accurate NMR Structures Through Minimization of an Extended Hybrid Energy
    Structure, Vol. 16, No. 9. (10 September 2008), pp. 1305-1312.
    by Michael Nilges, Aymeric Bernard, Benjamin Bardiaux, Thérèse Malliavin, Michael Habeck, Wolfgang Rieping
    posted to nmr comparative_model by barry to the group McCammon on 2008-09-09 22:35:15 as * along with 1 group structural_bioinformatics
  • ATP-binding cassette transporters in Escherichia coli.
    Biochimica et biophysica acta, Vol. 1778, No. 9. (September 2008), pp. 1757-1771.
    by A Moussatova, C Kandt, ML O'Mara, DP Tieleman
    posted to membrane_simulations by abebe to the group McCammon on 2008-09-08 19:54:49 as **
  • The Membrane Potential and its Representation by a Constant Electric Field in Computer Simulations.
    Biophysical journal (18 July 2008)
    by Benoit Roux
    posted to membrane_simulations by abebe to the group McCammon on 2008-09-08 19:38:39 as **** along with 1 person dimka
  • 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 3 people and 2 groups chad_davis 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 4 people and 1 group Zephyrus msierk Ema cmmorel Roswell Cancer Crosstalk
  • 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 3 people vahmurk 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 2 people and 1 group xdeupi merj LabCompMed
  • 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 5 people A_Coletta_Thesis 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
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