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barry's protein_structure [236 articles]

Recent papers added to barry's library classified by the tag protein_structure. You can also see everyone's protein_structure.
  • 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 on 2008-07-07 23:55:32 as ** along with 1 person and 1 group marck structural_bioinformatics
  • A Simple Model of Backbone Flexibility Improves Modeling of Side-chain Conformational Variability
    Journal of Molecular Biology, Vol. 380, No. 4. (18 July 2008), pp. 757-774.
    by Gregory D Friedland, Anthony J Linares, Colin A Smith, Tanja Kortemme
    posted to protein_structure protein_dynamics by barry on 2008-06-30 17:35:43 as **
  • notes 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 on 2008-06-10 22:34:01 as read along with 2 groups structural_bioinformatics Bioinformatics
  • Structural Basis of the Honey Bee PBP Pheromone and pH-induced Conformational Change
    Journal of Molecular Biology, Vol. 380, No. 1. (27 June 2008), pp. 158-169.
    by Marion E Pesenti, Silvia Spinelli, Valérie Bezirard, Loïc Briand, Jean-Claude Pernollet, Mariella Tegoni, Christian Cambillau
    posted to protein_structure protein_dynamics docking by barry on 2008-06-09 17:43:48 as **
  • Structural dynamics of the microtubule binding and regulatory elements in the kinesin-like calmodulin binding protein
    Journal of Structural Biology, Vol. In Press, Corrected Proof
    by Maia V Vinogradova, Galina G Malanina, Vaka S Reddy, Anireddy S Reddy, Robert J Fletterick
    posted to protein_structure kinesin by barry on 2008-06-02 19:41:22 as **
  • notes Investigating protein dynamics in collective coordinate space.
    Curr Opin Struct Biol, Vol. 9, No. 2. (April 1999), pp. 164-169.
    by A Kitao, N Go
    posted to review protein_structure protein_dynamics pca nma md_simulation by barry on 2008-04-29 00:04:52 as ** along with 4 people and 1 group sobolevnrm choonpeng ttjoseph ffranca baker-group
  • notes Collective protein dynamics in relation to function
    Current Opinion in Structural Biology, Vol. 10, No. 2. (1 April 2000), pp. 165-169.
    by Herman JC Berendsen, Steven Hayward
    posted to review protein_structure protein_dynamics pca nma md_simulation by barry on 2008-04-29 00:03:09 as **
  • 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 on 2008-04-17 19:15:44 as *** along with 2 people and 3 groups paulschlesinger sobolevnrm McCammon structural_bioinformatics baker-group
  • 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 on 2008-03-31 18:11:48 as *** along with 6 people and 3 groups cchang higueruelo choonpeng cactus sobolevnrm CameronNeylon group McCammon structural_bioinformatics
  • 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 on 2008-03-21 02:54:55 as * along with 1 group structural_bioinformatics
  • 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 protein_evolution protein_structure by barry on 2008-03-20 17:04:58 as ***** along with 1 person and 1 group cdeane structural_bioinformatics
  • Protein interactions in human genetic diseases
    Genome Biology, Vol. 9, No. 1. (2008)
    by Benjamin S Bockler, Alex Bateman
    posted to protein_protein protein_structure by barry on 2008-03-20 01:10:21 as read along with 9 people and 2 groups balicea frohike neils grahamc aconesa biomcgary barriot mingzhi mclarenv McCammon Bioinformatics
  • notes 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 protein_dynamics protein_structure by barry on 2008-03-20 00:43:49 as ** along with 3 people and 2 groups sobolevnrm jlh64 scienbox McCammon baker-group
  • 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 on 2008-03-20 00:40:27 as ** along with 7 people and 2 groups wilbur friendpine neils sobolevnrm mingzhi penpen926 scienbox structural_bioinformatics baker-group
  • Transitive homology-guided structural studies lead to discovery of Cro proteins with 40% sequence identity but different folds
    Proceedings of the National Academy of Sciences, Vol. 105, No. 7. (19 February 2008), pp. 2343-2348.
    by Christian G Roessler, Branwen M Hall, William J Anderson, Wendy M Ingram, Sue A Roberts, William R Montfort, Matthew H Cordes
    posted to fold_space protein_engineering protein_sequence protein_structure by barry on 2008-03-20 00:33:52 as ** along with 2 people and 1 group cactus sobolevnrm baker-group
  • Nucleotide-Mediated Conformational Changes of Monomeric Actin and Arp3 Studied by Molecular Dynamics Simulations.
    J Mol Biol (28 November 2007)
    by Paul Dalhaimer, Thomas D D Pollard, Brad J J Nolen
    posted to actin arp3 md_simulation protein_structure subfamily by barry on 2008-01-14 19:48:54 as ****
  • The AAA+ superfamily -- a myriad of motions
    Current Opinion in Structural Biology, Vol. 17, No. 6. (December 2007), pp. 641-652.
    by Paul A Tucker, Laszlo Sallai
    posted to aaa protein_structure review by barry on 2007-12-04 23:05:50 as *** along with 1 person cactus
  • 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 on 2007-12-04 22:56:25 as ** along with 7 people and 3 groups higueruelo LamBras aqeel ruvido cactus sobolevnrm jennifermbui structural_bioinformatics 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 on 2007-12-04 22:41:13 as * along with 2 people and 1 group bicko chad_davis structural_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 on 2007-10-31 21:53:37 as read along with 5 people and 2 groups choonpeng cactus sobolevnrm jlh64 melting structural_bioinformatics 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 on 2007-10-26 22:44:54 as **** along with 5 people and 2 groups GermanErlenkamp allmensch daevans sobolevnrm LamBras structural_bioinformatics baker-group
  • HingeProt: Automated prediction of hinges in protein structures
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Ugur Emekli, Dina Schneidman-Duhovny, Haim J Wolfson, Ruth Nussinov, Turkan Haliloglu
    posted to clustering hinge_motion nma protein_structure by barry on 2007-09-27 19:28:36 as read along with 3 people and 1 group higueruelo sobolevnrm willpitt baker-group
  • Exploring the range of protein flexibility, from a structural proteomics perspective
    Current Opinion in Chemical Biology, Vol. 8, No. 1. (February 2004), pp. 14-19.
    by Mark Gerstein, Nathaniel Echols
    posted to protein_dynamics protein_structure review by barry on 2007-09-27 19:19:21 as read
  • 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 comparative_model md_simulation nma protein_structure structure_refinement by barry on 2007-09-27 18:43:03 as read along with 1 person and 2 groups sobolevnrm structural_bioinformatics baker-group
  • 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 on 2007-09-22 23:29:36 as ***** along with 2 groups structural_bioinformatics Bioinformatics
  • Molecular basis for specificity in the druggable kinome: sequence-based analysis
    Bioinformatics, Vol. 23, No. 5. (March 2007), pp. 563-572.
    by Chen, Jianping, Zhang, Xi
    posted to dehydron hbond kinases protein_structure by barry on 2007-09-14 19:21:35 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • Localization of protein-binding sites within families of proteins.
    Protein Sci, Vol. 14, No. 9. (September 2005), pp. 2350-2360.
    by D Korkin, FP Davis, A Sali
    posted to protein_protein protein_sequence protein_structure by barry on 2007-09-14 01:51:37 as ** along with 5 people and 4 groups wilbur tjimenez bicko chad_davis marcius structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
  • How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues.
    Biophys J, Vol. 88, No. 3. (March 2005), pp. 1552-1559.
    by T Haliloglu, O Keskin, B Ma, R Nussinov
    posted to nma protein_protein protein_structure by barry on 2007-09-13 18:55:42 as ** along with 4 people and 2 groups baaden aqeel eweaver choonpeng structural_bioinformatics Bioinformatics
  • Dehydron: a structurally encoded signal for protein interaction.
    Biophys J, Vol. 85, No. 3. (September 2003), pp. 1914-1928.
    by A Fernández, R Scott
    posted to dehydron hbond protein_packing protein_protein protein_structure by barry on 2007-09-13 18:45:52 as ** along with 2 people and 2 groups BragilMassoud Evangelia structural_bioinformatics Bioinformatics
  • Insufficiently dehydrated hydrogen bonds as determinants of protein interactions.
    Proc Natl Acad Sci U S A, Vol. 100, No. 1. (7 January 2003), pp. 113-118.
    by A Fernández, HA Scheraga
    posted to dehydron hbond protein_packing protein_protein protein_structure by barry on 2007-09-13 18:45:36 as **** along with 1 person and 2 groups BragilMassoud structural_bioinformatics Bioinformatics
  • On the precision of calculated solvent-accessible surface areas
    Acta Crystallographica Section D Biological Crystallography
    by Novotny
    posted to protein_structure sas solvent by barry on 2007-09-08 00:50:42 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • Detecting similarities among distant homologous proteins by comparison of domain flexibilities
    Protein Engineering, Design and Selection (30 June 2007), gzm021.
    by Alessandro Pandini, Giancarlo Mauri, Annalisa Bordogna, Laura Bonati
    posted to protein_dynamics protein_structure by barry on 2007-09-05 01:57:38 as * along with 2 people and 2 groups edvin aqeel structural_bioinformatics Bioinformatics
  • Evolutionary Conservation of Protein Backbone Flexibility
    Journal of Molecular Evolution, Vol. 63, No. 4. (14 October 2006), pp. 448-457.
    by Sandra Maguid, Sebastián Fernández-Alberti, Gustavo Parisi, Julián Echave
    posted to nma protein_dynamics protein_structure by barry on 2007-09-05 01:48:20 as ** along with 2 people and 2 groups edvin jlh64 structural_bioinformatics Bioinformatics
  • Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces.
    Proc Natl Acad Sci U S A, Vol. 100, No. 10. (13 May 2003), pp. 5772-5777.
    by B Ma, T Elkayam, H Wolfson, R Nussinov
    posted to hot_spots protein_protein protein_sequence protein_structure by barry on 2007-09-04 19:49:40 as ** along with 8 people and 2 groups mdimmic bicko lyongu nickolay choonpeng cjeans carlescorbi ladab structural_bioinformatics Bioinformatics
  • Computational Design of a Single Amino Acid Sequence that Can Switch between Two Distinct Protein Folds.
    J Am Chem Soc, Vol. 128, No. 4. (1 February 2006), pp. 1154-1161.
    by XI Ambroggio, B Kuhlman
    posted to protein_design protein_dynamics protein_sequence protein_structure by barry on 2007-09-04 19:32:05 as ** along with 5 people and 2 groups ca3295 shuns jwm kevinchannon bethbromley structural_bioinformatics Bioinformatics
  • Optimization of specificity in a cellular protein interaction network by negative selection.
    Nature, Vol. 426, No. 6967. (11 December 2003), pp. 676-680.
    by A Zarrinpar, SH Park, WA Lim
    posted to protein_design protein_evolution protein_protein protein_sequence protein_structure by barry on 2007-09-04 19:25:04 as ** along with 3 people and 2 groups paolomarcatili grahamc cjeans structural_bioinformatics Bioinformatics
  • Convergent Evolution of Enzyme Active Sites Is not a Rare Phenomenon
    Journal of Molecular Biology, Vol. 372, No. 3. (21 September 2007), pp. 817-845.
    by Pier F Gherardini, Mark N Wass, Manuela Helmer-Citterich, Michael J Sternberg
    posted to convergent_evolution protein_evolution protein_structure by barry on 2007-08-31 19:04:36 as * along with 6 people and 2 groups sim82 tjimenez jjray chad_davis tny Minty structural_bioinformatics Bioinformatics
  • Comparison of side chain interactions performed by structurally equivalent residues in homologous protein structures
    Comput. Appl. Biosci., Vol. 11, No. 6. (1 December 1995), pp. 577-581.
    by Domenico Bordo
    posted to hbond protein_structure by barry on 2007-08-27 20:00:38 as * along with 2 groups structural_bioinformatics Bioinformatics
  • Characterization of Protein Conformational States by Normal-Mode Frequencies
    J. Am. Chem. Soc. (23 August 2007)
    by BA Hall, SL Kaye, A Pang, R Perera, PC Biggin
    posted to clustering md_simulation nma pca protein_structure by barry on 2007-08-27 19:15:41 as **** along with 4 people and 3 groups LamBras aqeel choonpeng sobolevnrm structural_bioinformatics Bioinformatics baker-group
  • How Well Can We Understand Large-Scale Protein Motions Using Normal Modes of Elastic Network Models?
    Biophys J (4 May 2007)
    by Lei Yang, Guang Song, Robert L L Jernigan
    posted to correlated_motions nma protein_dynamics protein_structure by barry on 2007-08-13 19:53:33 as ** along with 3 people and 2 groups aqeel choonpeng willpitt structural_bioinformatics Bioinformatics
  • Protein Flexibility and Mobility in Structure-Based Drug Design
    pp. 455-476.
    by Aqeel Ahmed
    posted to docking drug_design protein_dynamics protein_ligand protein_structure review by barry on 2007-08-13 19:47:46 as * along with 2 groups structural_bioinformatics Bioinformatics
  • Phylogeny of protein-folding trajectories reveals a unique pathway to native structure.
    Proc Natl Acad Sci U S A, Vol. 101, No. 51. (21 December 2004), pp. 17658-17663.
    by M Ota, M Ikeguchi, A Kidera
    posted to clustering contacts md_simulation protein_folding protein_structure by barry on 2007-08-10 18:38:42 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • Unfolding Pathways of Goat [alpha]-Lactalbumin as Revealed in Multiple Alignment of Molecular Dynamics Trajectories
    Journal of Molecular Biology, Vol. 371, No. 5. (31 August 2007), pp. 1354-1364.
    by Tomotaka Oroguchi, Mitsunori Ikeguchi, Motonori Ota, Kunihiro Kuwajima, Akinori Kidera
    posted to clustering contacts md_simulation protein_folding protein_structure by barry on 2007-08-10 18:36:13 as ** along with 1 person and 2 groups choonpeng structural_bioinformatics Bioinformatics
  • Predicting Absolute Ligand Binding Free Energies to a Simple Model Site
    Journal of Molecular Biology, Vol. 371, No. 4. (24 August 2007), pp. 1118-1134.
    by David L Mobley, Alan P Graves, John D Chodera, Andrea C Mcreynolds, Brian K Shoichet, Ken A Dill
    posted to docking protein_ligand protein_structure by barry on 2007-08-06 18:14:06 as ** along with 4 people and 3 groups insilico daevans superpyrin dmobley structural_bioinformatics Bioinformatics Computer Aided Drug Design
  • Structure of Human Eg5 in Complex with a New Monastrol-based Inhibitor Bound in the R Configuration
    J. Biol. Chem., Vol. 282, No. 13. (30 March 2007), pp. 9740-9747.
    by Isabel Garcia-Saez, Salvatore Debonis, Roman Lopez, Fernando Trucco, Bernard Rousseau, Pierre Thuery, Frank Kozielski
    posted to kinesin molecular_motors monastrol protein_structure by barry on 2007-07-27 02:03:03 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • Evolution of Function in the “Two Dinucleotide Binding Domains” Flavoproteins
    PLoS Computational Biology, Vol. 3, No. 7. (1 July 2007), e121.
    by Sunil Ojha, Elaine C Meng, Patricia C Babbitt
    posted to fad protein_design protein_evolution protein_structure by barry on 2007-07-20 18:33:27 as *** along with 3 people and 2 groups Einat zwang mdimon structural_bioinformatics Bioinformatics
  • A new method for estimating the importance of hydrophobic groups in the binding site of a protein.
    J Med Chem, Vol. 48, No. 4. (24 February 2005), pp. 1069-1078.
    by MD Kelly, RL Mancera
    posted to bioinf_methods docking hydrophobic protein_ligand protein_structure by barry on 2007-07-19 18:29:38 as ** along with 3 people and 2 groups nickolay blackbart ladab structural_bioinformatics Bioinformatics
  • notes Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
    Acta Crystallographica Section D: Biological Crystallography, Vol. 60, No. 1. (01 December 2004), pp. 2256-2268.
    by Krissinel, , Henrick,
    posted to bioinf_methods graph protein_structure structure_comparison by barry on 2007-07-13 19:39:15 as read along with 3 people and 4 groups jwm analogAI robert structural_bioinformatics Radiation_Damage Stressosome Bioinformatics
  • Geometric criteria of hydrogen bonds in proteins and identification of "bifurcated" hydrogen bonds.
    Protein Eng, Vol. 15, No. 5. (May 2002), pp. 359-363.
    by IY Torshin, IT Weber, RW Harrison
    posted to hbond protein_structure by barry on 2007-06-21 22:57:54 as * along with 2 people and 3 groups medic0747 sobolevnrm structural_bioinformatics Bioinformatics baker-group
  • notes Hydrogen bonding in globular proteins
    Progress in Biophysics and Molecular Biology, Vol. 44, No. 2. (1984), pp. 97-179.
    by EN Baker, RE Hubbard
    posted to hbond protein_structure review by barry on 2007-06-21 22:53:50 as read along with 2 groups structural_bioinformatics Bioinformatics
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