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Group: structural_bioinformatics - library [1287 articles]

Recent papers posted by members of the structural_bioinformatics group
  • The importance of stupidity in scientific research
    J Cell Sci, Vol. 121, No. 11. (1 June 2008), 1771.
    by Martin A Schwartz
    posted to essay career advice by barry to the group structural_bioinformatics on 2008-07-16 22:25:46 as **** along with 2 people and 1 group arindrartow dullhunk McCammon
  • 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 titration protein-protein binding by barry to the group structural_bioinformatics on 2008-07-08 01:26:01 as ** along with 4 people and 2 groups bicko chad_davis sobolevnrm RamuAnandakrishnan McCammon baker-group
  • X-ray structure of a prokaryotic pentameric ligand-gated ion channel
    Nature (05 March 2008)
    by Ricarda JC Hilf, Raimund Dutzler
    posted to ion_channel achr by barry to the group structural_bioinformatics on 2008-07-08 01:24:17 as ** along with 2 people and 1 group neils jmccammon McCammon
  • 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 replica_exchange md_simulation by barry to the group structural_bioinformatics on 2008-07-08 01:17:17 as ** along with 3 people and 2 groups loison sobolevnrm agrossfield McCammon 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 protein_ligand drug_discovery by barry to the group structural_bioinformatics on 2008-07-08 01:14:49 as ** along with 1 person and 1 group jmccammon McCammon
  • 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 protein-ligand md_simulation free_energy binding by barry to the group structural_bioinformatics on 2008-07-08 01:12:03 as ** along with 3 people and 2 groups sobolevnrm jmccammon biehl McCammon baker-group
  • 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 solvation protein-ligand md_simulation free_energy by barry to the group structural_bioinformatics on 2008-07-08 01:11:30 as ** along with 2 people and 2 groups sobolevnrm jmccammon baker-group McCammon
  • 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 protein-protein binding by barry to the group structural_bioinformatics on 2008-07-08 00:52:29 as ** along with 4 people and 2 groups cchang jmccammon higueruelo paulschlesinger group McCammon
  • 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 structural_bioinformatics on 2008-07-08 00:51:34 as ** along with 1 group McCammon
  • 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 replica_exchange coarse_grain by barry to the group structural_bioinformatics on 2008-07-08 00:49:57 as ** along with 3 people and 1 group jmccammon zwang RamuAnandakrishnan McCammon
  • notes BIOCHEMISTRY: Metamorphic Proteins
    Science, Vol. 320, No. 5884. (27 June 2008), pp. 1725-1726.
    by Alexey G Murzin
    posted to review protein_structure protein_dynamics by barry to the group structural_bioinformatics on 2008-07-07 23:55:32 as ** along with 1 person marck
  • Homology-based modeling of 3D structures of protein-protein complexes using alignments of modified sequence profiles.
    International journal of biological macromolecules (21 May 2008)
    by Petras J J Kundrotas, Marc F F Lensink, Emil Alexov
    posted to structure proj_assembly modelling data_integration complexes binding alignment algorithm by chad_davis to the group structural_bioinformatics on 2008-06-29 11:15:36 as **
  • Mapping the Nucleotide and Isoform-Dependent Structural and Dynamical Features of Ras Proteins
    Structure, Vol. 16, No. 6. (11 June 2008), pp. 885-896.
    by Alemayehu A Gorfe, Barry J Grant, Andrew J Mccammon
    posted to ras protein_structure protein_dynamics pca ntpases mine md_simulation by barry to the group structural_bioinformatics on 2008-06-10 22:34:01 as read along with 1 group Bioinformatics
  • Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy.
    Journal of structural biology, Vol. 149, No. 2. (February 2005), pp. 191-203.
    by M Topf, ML Baker, B John, W Chiu, A Sali
    posted to structure proj_assembly modelling em data_integration complexes alignment algorithm by chad_davis to the group structural_bioinformatics on 2008-05-28 10:37:06 as **
  • notes Structural modeling of protein interactions by analogy: application to PSD-95.
    PLoS Comput Biol, Vol. 2, No. 11. (10 November 2006)
    by D Korkin, FP Davis, F Alber, T Luong, MY Shen, V Lucic, MB Kennedy, A Sali
    posted to structure proj_assembly modelling docking complexes binding algorithm by chad_davis to the group structural_bioinformatics on 2008-05-28 10:32:13 as *** along with 1 person bicko
  • Prediction of disordered regions in proteins based on the meta approach
    Bioinformatics (20 April 2008), btn195.
    by Takashi Ishida, Kengo Kinoshita
    posted to structure proj_disocons ensemble disorder classification algorithm by chad_davis to the group structural_bioinformatics on 2008-04-28 09:47:26 as ***** along with 1 person niallhaslam
  • Molecular Dynamics Simulation of the Escherichia coli NikR Protein: Equilibrium Conformational Fluctuations Reveal Interdomain Allosteric Communication Pathways
    Journal of Molecular Biology, Vol. In Press, Corrected Proof
    by Michael J Bradley, Peter T Chivers, Nathan A Baker
    posted to md_simulation allosteric by barry to the group structural_bioinformatics on 2008-04-27 22:02:29 as * along with 2 people and 1 group skoddet sobolevnrm baker-group
  • 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 protein_dynamics protein_structure review smd by barry to the group structural_bioinformatics on 2008-04-17 19:15:44 as *** along with 2 people and 2 groups paulschlesinger sobolevnrm McCammon baker-group
  • notes Tracing evolutionary pressure
    Bioinformatics, Vol. 24, No. 7. (1 April 2008), pp. 908-915.
    by Kai Ye, Gert Vriend, Adriaan P Ijzerman
    posted to bioinf_methods phylogeny protein_evolution protein_sequence residue_annotation by barry to the group structural_bioinformatics on 2008-04-11 19:13:22 as *** along with 1 person and 1 group sunhwan 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 protein_dynamics protein_structure review by barry to the group structural_bioinformatics on 2008-03-31 18:11:48 as *** along with 6 people and 2 groups cchang higueruelo choonpeng cactus sobolevnrm CameronNeylon group McCammon
  • STRUCTURAL BIOLOGY: Researchers Hone Their Homology Tools
    Science, Vol. 319, No. 5870. (21 March 2008), 1612.
    by Robert F Service
    posted to comparative_model protein_structure by barry to the group structural_bioinformatics on 2008-03-21 02:54:55 as *
  • notes Discrimination between Distant Homologs and Structural Analogs: Lessons from Manually Constructed, Reliable Data Sets
    Journal of Molecular Biology, Vol. 377, No. 4. (4 April 2008), pp. 1265-1278.
    by Hua Cheng, Bong-Hyun Kim, Nick V Grishin
    posted to no-tag by barry to the group structural_bioinformatics on 2008-03-20 17:04:58 as ***** along with 1 person cdeane
  • Analysis of the residue-residue coevolution network and the functionally important residues in proteins
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by Byung-Chul Lee, Keunwan Park, Dongsup Kim
    posted to correlated_mutations protein_sequence protein_structure by barry to the group structural_bioinformatics on 2008-03-20 00:40:27 as ** along with 7 people and 1 group wilbur friendpine neils sobolevnrm mingzhi penpen926 scienbox baker-group
  • 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 structural_bioinformatics on 2008-03-20 00:05:53 as **** along with 11 people and 2 groups joseph_x_zhou ucbcjbm aalibes jwm aprasad dgront zwang sobolevnrm davidlott msuarezdiez scienbox McCammon baker-group
  • Background frequencies for residue variability estimates: BLOSUM revisited
    BMC Bioinformatics, Vol. 8 (27 December 2007), 488.
    by I Mihalek, I Res, O Lichtarge
    posted to algorithm alignment evolution statistics by chad_davis to the group structural_bioinformatics on 2008-02-26 10:43:45 as ** along with 5 people bicko gokhan rabio laughcry biehl
  • An iterative knowledge-based scoring function for protein-protein recognition
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by Sheng-You Huang, Xiaoqin Zou
    posted to algorithms binding competition docking phd statistics structure by chad_davis to the group structural_bioinformatics on 2008-02-05 09:54:41 as *****
  • Coarse-grained models for simulations of multi-protein complexes: Application to ubiquitin binding
    Journal of Molecular Biology, Vol. In Press, Accepted Manuscript
    by Young C Kim, Gerhard Hummer
    posted to coarse-grained protein_protein ubiqutin by barry to the group structural_bioinformatics on 2008-01-10 19:41:25 as ** along with 3 people and 2 groups sobolevnrm iantunbridge mikaellund Bioinformatics baker-group
  • 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 allosteric protein_dynamics protein_structure review by barry to the group structural_bioinformatics on 2007-12-04 22:56:25 as ** along with 7 people and 2 groups higueruelo LamBras aqeel ruvido cactus sobolevnrm jennifermbui Bioinformatics baker-group
  • Comparative Analysis of Protein Structure Alignments
    BMC Structural Biology, Vol. 7 (26 July 2007), 50.
    by Gabriele Mayr, Francisco S Domingues, Peter Lackner
    posted to protein_structure review structure_comparison by barry to the group structural_bioinformatics on 2007-12-04 22:41:13 as * along with 2 people bicko chad_davis
  • Correlated substitution analysis and the prediction of amino acid structural contacts
    Brief Bioinform (13 November 2007), bbm052.
    by David S Horner, Walter Pirovano, Graziano Pesole
    posted to correlated_mutations review by barry to the group structural_bioinformatics on 2007-11-27 23:34:46 as * along with 2 people and 2 groups zwang sobolevnrm Bioinformatics baker-group
  • Wordom: a program for efficient analysis of molecular dynamics simulations
    Bioinformatics, Vol. 23, No. 19. (1 October 2007), pp. 2625-2627.
    by Michele Seeber, Marco Cecchini, Francesco Rao, Giovanni Settanni, Amedeo Caflisch
    posted to bioinf_methods md_simulation by barry to the group structural_bioinformatics on 2007-11-27 23:33:01 as ** along with 6 people and 1 group jyuh tmmurali choonpeng hmk sobolevnrm LamBras baker-group
  • Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism
    Proceedings of the National Academy of Sciences (13 November 2007), 0706443104.
    by Karunesh Arora, Charles L Brooks
    posted to allosteric kinases md_simulation by barry to the group structural_bioinformatics on 2007-11-27 23:23:59 as ** along with 5 people and 1 group allmensch cactus sobolevnrm jlh64 karunesh baker-group
  • Biskit -- a software platform for structural bioinformatics.
    Bioinformatics, Vol. 23, No. 6. (15 March 2007), pp. 769-770.
    by R Gruenberg, M Nilges, J Leckner
    posted to protein_structure tools by aalibes to the group structural_bioinformatics on 2007-11-14 17:00:05 as read along with 3 people jyuh bicko chad_davis
  • Functional Specificity Lies within the Properties and Evolutionary Changes of Amino Acids
    Journal of Molecular Biology, Vol. 373, No. 3. (26 October 2007), pp. 801-810.
    by Saikat Chakrabarti, Stephen H Bryant, Anna R Panchenko
    posted to clustering protein_sequence subfamily by barry to the group structural_bioinformatics on 2007-10-31 21:58:02 as ** along with 3 people and 1 group Einat biehl mingzhi Bioinformatics
  • Predicting Allosteric Communication in Myosin via a Pathway ofConserved Residues
    Journal of Molecular Biology, Vol. In Press, Accepted Manuscript
    by Susan Tang, Jung-Chi Liao, Alexander R Dunn, Russ B Altman, James A Spudich, Jeanette P Schmidt
    posted to allosteric molecular_motors myosin protein_sequence protein_structure sequence_comparison by barry to the group structural_bioinformatics on 2007-10-31 21:53:37 as read along with 5 people and 1 group choonpeng cactus sobolevnrm jlh64 melting baker-group
  • Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms
    J. Chem. Theory Comput. (6 October 2007)
    by J Shao, SW Tanner, N Thompson, TE Cheatham
    posted to clustering md_simulation protein_structure by barry to the group structural_bioinformatics on 2007-10-26 22:44:54 as **** along with 5 people and 1 group GermanErlenkamp allmensch daevans sobolevnrm LamBras baker-group
  • Determination of electrostatic interaction energies and protonation state populations in enzyme active sites
    Journal of Molecular Biology, Vol. In Press, Accepted Manuscript
    by Chresten R Sondergaard, Lawrence P Mcintosh, Gianluca Pollastri, Jens E Nielsen
    posted to electrostatics solvent by barry to the group structural_bioinformatics on 2007-10-26 22:39:25 as ** along with 2 people and 1 group sobolevnrm skoddet baker-group
  • Supercharging Proteins Can Impart Unusual Resilience
    J. Am. Chem. Soc., Vol. 129, No. 33. (22 August 2007), pp. 10110-10112.
    by MS Lawrence, KJ Phillips, DR Liu
    posted to electrostatics journal_club protein_design protein_evolution protein_folding by barry to the group structural_bioinformatics on 2007-10-26 22:37:58 as read along with 2 people and 2 groups samjlord sobolevnrm moernerlab baker-group
  • Knowledge-based prediction of DNA atomic structure from nucleic sequence.
    Genome Inform, Vol. 16, No. 2. (2005), pp. 12-21.
    by MJ Araúzo-Bravo, A Sarai
    posted to bioinformatics dna dna_structure by shantanu to the group structural_bioinformatics on 2007-10-18 17:40:37 as ** along with 1 person and 1 group echcram Bioinformatics
  • Complementarity of Structure Ensembles in Protein-Protein Binding
    Structure, Vol. 12, No. 12. (December 2004), pp. 2125-2136.
    by Raik Gruenberg, Johan Leckner, Michael Nilges
    posted to md_simulation protein_dynamics protein_protein by barry to the group structural_bioinformatics on 2007-10-02 03:05:14 as read along with 3 people and 2 groups lna allmensch cursonivel1 Bioinformatics cursonivel1
  • Molecular Dynamic Simulations of Cisplatin- and Oxaliplatin-d(GG) Intrastand Cross-links Reveal Differences in their Conformational Dynamics.
    J Mol Biol (23 August 2007)
    by Shantanu Sharma, Peng Gong, Brenda Temple, Debadeep Bhattacharyya, Nikolay V V Dokholyan, Stephen G G Chaney
    posted to anticancer cancer cisplatin dna_structure drug oxaliplatin publications by shantanu to the group structural_bioinformatics on 2007-09-30 18:06:41 as ***** along with 3 groups MathBio Bioinformatics Computational-Neurobiology
  • Dihedral angle principal component analysis of molecular dynamics simulations
    The Journal of Chemical Physics, Vol. 126, No. 24. (2007)
    by Alexandros Altis, Phuong H Nguyen, Rainer Hegger, Gerhard Stock
    posted to md_simulation pca torsion_angles by barry to the group structural_bioinformatics on 2007-09-27 20:06:59 as *** along with 2 people ruvido nh
  • Assessing predictions of protein-protein interaction: the CAPRI experiment.
    Protein Sci, Vol. 14, No. 2. (February 2005), pp. 278-283.
    by J Janin
    posted to docking protein_protein by barry to the group structural_bioinformatics on 2007-09-27 19:26:18 as read along with 3 people bicko ima drastic
  • Representing receptor flexibility in ligand docking through relevant normal modes.
    J Am Chem Soc, Vol. 127, No. 26. (6 July 2005), pp. 9632-9640.
    by CN Cavasotto, JA Kovacs, RA Abagyan
    posted to docking nma by barry to the group structural_bioinformatics on 2007-09-27 19:13:39 as read along with 6 people and 2 groups BragilMassoud apaydin aqeel yongzhao kazemi LamBras Bioinformatics TSRI_MGL
  • Sampling of near-native protein conformations during protein structure refinement using a coarse-grained model, normal modes, and molecular dynamics simulations
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Andrew W Stumpff-Kane, Katarzyna Maksimiak, Michael S Lee, Michael Feig
    posted to no-tag by barry to the group structural_bioinformatics on 2007-09-27 18:43:14 as read along with 1 person and 1 group sobolevnrm baker-group
  • Protein-Protein Docking with Backbone Flexibility
    Journal of Molecular Biology, Vol. 373, No. 2. (19 October 2007), pp. 503-519.
    by Chu Wang, Philip Bradley, David Baker
    posted to docking protein_protein by barry to the group structural_bioinformatics on 2007-09-27 17:40:34 as *** along with 3 people and 1 group jwm xdeupi Ema Bioinformatics
  • Signal Propagation in Proteins and Relation to Equilibrium Fluctuations
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e172.
    by Chakra Chennubhotla, Ivet Bahar
    posted to allosteric correlated_motions nma protein_dynamics protein_structure time_series_analysis by barry to the group structural_bioinformatics on 2007-09-22 23:29:36 as ***** along with 1 group Bioinformatics
  • A complex profile of protein elongation: translating chemical energy into molecular movement
    Structure, Vol. 4, No. 3. (March 1996), pp. 229-238.
    by Kenton Abel, Frances Jurnak
    posted to review ntpases g_proteins ef-tu by barry to the group structural_bioinformatics on 2007-09-20 23:01:17 as ** along with 1 group Bioinformatics
  • The nonconserved wrapping of conserved protein folds reveals a trend toward increasing connectivity in proteomic networks.
    Proc Natl Acad Sci U S A, Vol. 101, No. 9. (2 March 2004), pp. 2823-2827.
    by A Fernández, R Scott, RS Berry
    posted to hbond dehydron by barry to the group structural_bioinformatics on 2007-09-20 00:28:04 as * along with 1 person and 1 group baaden Bioinformatics
  • Extent of Hydrogen-Bond Protection in Folded Proteins: A Constraint on Packing Architectures
    Biophys. J., Vol. 83, No. 5. (1 November 2002), pp. 2475-2481.
    by Ariel Fernandez, Stephen R Berry
    posted to hbond dehydron by barry to the group structural_bioinformatics on 2007-09-20 00:25:21 as * along with 1 group Bioinformatics
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