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Group: structural_bioinformatics - with tag protein_structure [390 articles]

Neue Artikel von Mitliedern der Gruppe structural_bioinformatics Gruppe with tag protein_structure
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  • Can Morphing Methods Predict Intermediate Structures?
    Journal of molecular biology (30 October 2008)
    by Dahlia R R Weiss, Michael Levitt
    posted to protein_structure by barry to the group structural_bioinformatics on 2008-11-14 02:30:33 as ** along with 1 person and 1 group apaydin McCammon
  • tCONCOORD-GUI: Visually supported conformational sampling of bioactive molecules.
    Journal of computational chemistry (22 October 2008)
    by Daniel Seeliger, Bert L L De Groot
    posted to protein_structure protein_dynamics bioinf_methods by barry to the group structural_bioinformatics on 2008-10-25 17:55:41 as **
  • The 'glutamate switch' provides a link between ATPase activity and ligand binding in AAA+ proteins.
    Nature structural & molecular biology (12 October 2008)
    by Xiaodong Zhang, Dale B B Wigley
    posted to protein_structure aaa by barry to the group structural_bioinformatics on 2008-10-18 09:31:17 as ** along with 1 person and 1 group abebe McCammon
  • 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 structural_bioinformatics on 2008-10-05 19:12:36 as ** along with 2 groups McCammon Bioinformatics
  • Structural biology by NMR: structure, dynamics, and interactions.
    PLoS computational biology, Vol. 4, No. 9. (September 2008)
    by PR Markwick, T Malliavin, M Nilges
    posted to review protein_structure nmr by barry to the group structural_bioinformatics on 2008-10-02 20:04:45 as ** along with 7 people betainverse bmduggan pengchy raik ruvido zwang laurabailey
  • 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 structural_bioinformatics on 2008-10-02 19:46:30 as ** along with 3 people and 2 groups bpb zwang cmzmasek McCammon 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 protein_structure protein_dynamics allosteric by barry to the group structural_bioinformatics on 2008-10-02 18:34:06 as ** along with 1 person and 1 group TonyIvetac McCammon
  • Structure-Guided Comparative Analysis of Proteins: Principles, Tools, and Applications for Predicting Function
    PLoS Comput Biol, Vol. 4, No. 9. (2008), e1000151.
    by Raja Mazumder, Sona Vasudevan
    posted to protein_structure protein_function by barry to the group structural_bioinformatics on 2008-09-26 21:48:09 as ** along with 9 people and 1 group i000 pengchy raik chad_davis zwang druvus reyez mdstobbe jameswasmuth Bioinformatics
  • 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 structural_bioinformatics on 2008-09-26 18:14:38 as *** along with 2 people and 2 groups aqeel mijam McCammon Bioinformatics
  • 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 structural_bioinformatics on 2008-09-08 17:53:09 as read along with 2 people and 2 groups cabbagesofdoom Ema McCammon Bioinformatics
  • Progress in Modeling of Protein Structures and Interactions
    Science, Vol. 310, No. 5748. (28 October 2005), pp. 638-642.
    by Ora Schueler-Furman, Chu Wang, Phil Bradley, Kira Misura, David Baker
    posted to comparative_model protein_protein protein_structure by barry to the group structural_bioinformatics on 2008-08-01 19:03:07 as ** along with 13 people and 2 groups thaliana jwm vavi bicko KyuhoLee marcius eweaver tny nickolay dgront rsantana mirzazadeh insectopalo BioinfoCIPF SGU-CIPF
  • notes BIOCHEMISTRY: Metamorphic Proteins
    Science, Vol. 320, No. 5884. (27 June 2008), pp. 1725-1726.
    by Alexey G Murzin
    posted to protein_dynamics protein_structure review by barry to the group structural_bioinformatics on 2008-07-07 23:55:32 as ** along with 1 person marck
  • 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 md_simulation mine ntpases pca protein_dynamics protein_structure ras by barry to the group structural_bioinformatics on 2008-06-10 22:34:01 as read along with 1 group 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 protein_dynamics protein_structure review smd by barry to the group structural_bioinformatics on 2008-04-17 19:15:44 as *** along with 4 people and 2 groups aqeel sobolevnrm paulschlesinger toerst baker-group McCammon
  • 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 choonpeng cactus sobolevnrm CameronNeylon higueruelo cchang McCammon group
  • 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 *
  • 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 neils sobolevnrm mingzhi penpen926 scienbox wilbur friendpine 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 8 people and 3 groups aqeel ruvido cactus sobolevnrm jennifermbui higueruelo LamBras jmccammon Bioinformatics baker-group McCammon
  • 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 1 person bicko
  • 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 4 people raik guhjy bicko chad_davis
  • 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 6 people and 2 groups oteri daevans sobolevnrm LamBras allmensch GermanErlenkamp Structural Biology Group TorVergata 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 to the group structural_bioinformatics on 2007-09-22 23:29:36 as ***** along with 1 group 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 protein_structure kinases hbond dehydron by barry to the group structural_bioinformatics on 2007-09-14 19:21:35 as ** along with 1 group 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_structure protein_sequence protein_protein by barry to the group structural_bioinformatics on 2007-09-14 01:51:37 as ** along with 4 people and 3 groups tjimenez bicko marcius wilbur 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 protein_structure protein_protein nma by barry to the group structural_bioinformatics on 2007-09-13 18:55:42 as ** along with 4 people and 1 group baaden aqeel eweaver choonpeng 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 protein_structure protein_protein protein_packing hbond dehydron by barry to the group structural_bioinformatics on 2007-09-13 18:45:52 as ** along with 2 people and 1 group BragilMassoud Evangelia 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 protein_structure protein_protein protein_packing hbond dehydron by barry to the group structural_bioinformatics on 2007-09-13 18:45:36 as **** along with 1 person and 1 group BragilMassoud Bioinformatics
  • On the precision of calculated solvent-accessible surface areas
    Acta Crystallographica Section D Biological Crystallography
    by Novotny
    posted to solvent sas protein_structure by barry to the group structural_bioinformatics on 2007-09-08 00:50:42 as ** along with 1 group 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_structure protein_dynamics by barry to the group structural_bioinformatics on 2007-09-05 01:57:38 as * along with 2 people and 1 group aqeel edvin 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 protein_structure protein_dynamics nma by barry to the group structural_bioinformatics on 2007-09-05 01:48:20 as ** along with 4 people and 1 group gisle jlh64 edvin tny 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 protein_structure protein_sequence protein_protein hot_spots by barry to the group structural_bioinformatics on 2007-09-04 19:49:40 as ** along with 8 people and 1 group mdimmic bicko lyongu nickolay choonpeng cjeans carlescorbi ladab 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_structure protein_sequence protein_dynamics protein_design by barry to the group structural_bioinformatics on 2007-09-04 19:32:05 as ** along with 5 people and 1 group shuns jwm kevinchannon bethbromley ca3295 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_structure protein_sequence protein_protein protein_evolution protein_design by barry to the group structural_bioinformatics on 2007-09-04 19:25:04 as ** along with 4 people and 1 group grahamc cjeans paolomarcatili phoenixzxl Bioinformatics
  • Design of Multi-Specificity in Protein Interfaces
    PLoS Computational Biology, Vol. 3, No. 8. (1 August 2007), e164.
    by Elisabeth L Humphris, Tanja Kortemme
    posted to protein_structure interface design by Einat to the group structural_bioinformatics on 2007-09-02 16:02:53 as ***** along with 7 people and 2 groups msuarezdiez jwm bicko dpollard Scis0000002 phoenixzxl marck Bioinformatics EisenLab
  • 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 protein_structure protein_evolution convergent_evolution by barry to the group structural_bioinformatics on 2007-08-31 19:04:36 as * along with 8 people and 1 group ucbcjbm tjimenez jjray chad_davis tny shung Minty sim82 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 protein_structure hbond by barry to the group structural_bioinformatics on 2007-08-27 20:00:38 as * along with 1 group 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 protein_structure pca nma md_simulation clustering by barry to the group structural_bioinformatics on 2007-08-27 19:15:41 as **** along with 5 people and 2 groups ubcg08l aqeel choonpeng sobolevnrm LamBras 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 protein_structure protein_dynamics nma correlated_motions by barry to the group structural_bioinformatics on 2007-08-13 19:53:33 as ** along with 3 people and 1 group aqeel choonpeng willpitt Bioinformatics
  • Protein Flexibility and Mobility in Structure-Based Drug Design
    pp. 455-476.
    by Aqeel Ahmed
    posted to review protein_structure protein_ligand protein_dynamics drug_design docking by barry to the group structural_bioinformatics on 2007-08-13 19:47:46 as * along with 1 group 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 protein_structure protein_folding md_simulation contacts clustering by barry to the group structural_bioinformatics on 2007-08-10 18:38:42 as ** along with 1 group 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 protein_structure protein_folding md_simulation contacts clustering by barry to the group structural_bioinformatics on 2007-08-10 18:36:13 as ** along with 1 person and 1 group choonpeng 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 protein_structure protein_ligand docking by barry to the group structural_bioinformatics on 2007-08-06 18:14:06 as ** along with 4 people and 2 groups insilico daevans superpyrin dmobley 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 protein_structure monastrol molecular_motors kinesin by barry to the group structural_bioinformatics on 2007-07-27 02:03:03 as ** along with 1 group 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 protein_structure protein_evolution protein_design fad by barry to the group structural_bioinformatics on 2007-07-20 18:33:27 as *** along with 4 people and 1 group pradiptaray Einat zwang mdimon 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 protein_structure protein_ligand hydrophobic docking bioinf_methods by barry to the group structural_bioinformatics on 2007-07-19 18:29:38 as ** along with 3 people and 1 group nickolay blackbart ladab Bioinformatics
  • 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 structure_comparison protein_structure graph bioinf_methods by barry to the group structural_bioinformatics on 2007-07-13 19:39:15 as read along with 3 people and 3 groups jwm analogAI robert Radiation_Damage Stressosome Bioinformatics
  • Clustering protein environments for function prediction: finding PROSITE motifs in 3D.
    BMC Bioinformatics, Vol. 8 Suppl 4 (2007)
    by S Yoon, JC Ebert, EY Chung, G De Micheli, RB Altman
    posted to structural_enviroment protein_structure active-site by Einat to the group structural_bioinformatics on 2007-07-01 13:56:21 as **** along with 1 person shadowman
  • Three-Dimensional Phylogeny Explorer: Distinguishing paralogs, lateral transfer, and violation of "molecular clock" assumption with 3D visualization
    BMC Bioinformatics, Vol. 8 (20 June 2007), 213.
    by Namshin Kim, Christopher Lee
    posted to protein_structure evolution by Einat to the group structural_bioinformatics on 2007-06-26 14:49:57 as ****
  • 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 protein_structure hbond by barry to the group structural_bioinformatics on 2007-06-21 22:57:54 as * along with 2 people and 2 groups medic0747 sobolevnrm Bioinformatics baker-group
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