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Group: structural_bioinformatics - library [1321 articles]

Recent papers posted by members of the structural_bioinformatics group
  • 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 structural_bioinformatics on 2008-10-05 18:59:32 as * along with 1 person and 1 group middledomain McCammon
  • 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 structural_bioinformatics on 2008-09-09 22:35:15 as * along with 1 group McCammon
  • Agonist-Induced Conformational Changes in Bovine Rhodopsin: Insight into Activation of G-Protein-Coupled Receptors
    Journal of Molecular Biology, Vol. 382, No. 2. (3 October 2008), pp. 539-555.
    by Supriyo Bhattacharya, Spencer E Hall, Nagarajan Vaidehi
    posted to gpcr by barry to the group structural_bioinformatics on 2008-08-29 18:52:34 as *
  • A comparison of common programming languages used in bioinformatics
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Mathieu Fourment, Michael Gillings
    posted to programming review by barry to the group structural_bioinformatics on 2008-08-21 18:01:49 as * along with 11 people and 1 group jamselem dullhunk laughcry ibuch urgi sci91078 renatomilani xili03 phoenixzxl jyuh chad_davis Bioinformatics
  • 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 allosteric md_simulation by barry to the group structural_bioinformatics on 2008-04-27 22:02:29 as * along with 2 people and 1 group sobolevnrm skoddet baker-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 *
  • 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 chad_davis bicko
  • 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 3 people and 2 groups zwang sobolevnrm Lombardo_7 Bioinformatics baker-group
  • 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
  • A Ras by Any Other Name
    Mol. Cell. Biol., Vol. 21, No. 5. (1 March 2001), pp. 1441-1443.
    by Dafna Bar-Sagi
    posted to review ras by barry to the group structural_bioinformatics on 2007-09-20 00:03:36 as * along with 1 group Bioinformatics
  • Molecular Determination by Electron Microscopy of the Dynein-Microtubule Complex Structure
    Journal of Molecular Biology, Vol. 372, No. 5. (5 October 2007), pp. 1320-1336.
    by Akihiro Narita, Naoko Mizuno, Masahide Kikkawa, Yuichiro Maeda
    posted to molecular_motors em dynein by barry to the group structural_bioinformatics on 2007-09-17 17:59:59 as * along with 1 group Bioinformatics
  • The Chemistry of Protein Catalysis
    Journal of Molecular Biology, Vol. 372, No. 5. (5 October 2007), pp. 1261-1277.
    by Gemma L Holliday, Daniel E Almonacid, John B Mitchell, Janet M Thornton
    posted to review catalytic_mechanism by barry to the group structural_bioinformatics on 2007-09-17 17:53:36 as * along with 7 people and 1 group ucbcjbm cjeans zwang grottenolm jwm sim82 gemmalholliday Bioinformatics
  • Analysis of Domain Movements in Glutamine-Binding Protein with Simple Models
    Biophys. J., Vol. 92, No. 4. (15 February 2007), pp. 1326-1335.
    by Ji G Su, Xiong Jiao, Ting G Sun, Chun H Li, Wei Z Chen, Cun X Wang
    posted to nma domain_motions by barry to the group structural_bioinformatics on 2007-09-13 18:57:46 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
  • Amino acid preferences at protein binding sites
    FEBS Letters, Vol. 349, No. 1. (25 July 1994), pp. 125-130.
    by Hugo O Villar, Lawrence M Kauvar
    posted to protein_sequence protein_protein by barry to the group structural_bioinformatics on 2007-09-04 20:17:20 as * along with 1 group 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 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
  • Achievement index climbs the ranks
    Nature, Vol. 448, No. 7155. (2007)
    by P Ball
    posted to career by barry to the group structural_bioinformatics on 2007-08-27 19:20:40 as * along with 1 person and 2 groups sobolevnrm Bioinformatics baker-group
  • Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking.
    J Mol Biol, Vol. 344, No. 3. (26 November 2004), pp. 781-795.
    by X Li, O Keskin, B Ma, R Nussinov, J Liang
    posted to protein_protein by barry to the group structural_bioinformatics on 2007-08-14 22:53:26 as * along with 10 people and 1 group baaden bicko nickolay j3xucite bluvsh1 xz grahamc Evangelia ladab paolomarcatili 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
  • 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
  • Phase diagram of microtubules
    Physical Review E, Vol. 50, No. 2. (1994), 1579.
    by Deborah K Fygenson, Erez Braun, Albert Libchaber
    posted to mts by barry to the group structural_bioinformatics on 2007-05-10 07:38:19 as * along with 1 group Bioinformatics
  • Locus control regions: coming of age at a decade plus.
    Trends Genet, Vol. 15, No. 10. (October 1999), pp. 403-408.
    by Q Li, S Harju, KR Peterson
    posted to promoter_identification gene_finding by ana to the group structural_bioinformatics on 2007-04-17 00:05:14 as * along with 1 group Bioinformatics
  • Mechanochemical Coupling in the Myosin Motor Domain. I. Insights from Equilibrium Active-Site Simulations
    PLoS Computational Biology, Vol. 3, No. 2. (1 February 2007), e21.
    by Haibo Yu, Liang Ma, Yang Yang, Qiang Cui
    posted to md_simulation molecular_motors myosin pmf by barry to the group structural_bioinformatics on 2007-02-12 23:41:33 as * along with 1 group Bioinformatics
  • Microarray data analysis: from disarray to consolidation and consensus
    Nature Reviews Genetics, Vol. 7, No. 1., pp. 55-65.
    by David B Allison, Xiangqin Cui, Grier P Page, Mahyar Sabripour
    posted to review microarrays by barry to the group structural_bioinformatics on 2007-01-18 18:58:17 as * along with 23 people and 1 group verdicchio jyuh textoris jfr Ayest balicea sterovetta lhonigberg acidwizard ronaldozhou vpschulz rmk schuylrp Garamonfok debasis GeeSharpMinor dimatura heliopais shikin minostro giovenko jo_davies aviad_work Bioinformatics
  • Exploration of the conformational space of myosin recovery stroke via molecular dynamics
    Biophysical Chemistry, Vol. 125, No. 1. (January 2007), pp. 127-137.
    by Hyung-June Woo
    posted to md_simulation myosin by barry to the group structural_bioinformatics on 2006-12-08 18:58:04 as * along with 1 group Bioinformatics
  • Molecular dynamics -- potential of mean force calculations as a tool for understanding ion permeation and selectivity in narrow channels
    Biophysical Chemistry, Vol. 124, No. 3. (1 December 2006), pp. 251-267.
    by Toby W Allen, Olaf S Andersen, Benoit Roux
    posted to ion_channels md_simulation pmf by barry to the group structural_bioinformatics on 2006-12-08 18:46:14 as * along with 2 people and 2 groups sobolevnrm ibuch Bioinformatics baker-group
  • An aspartate residue in yeast alcohol dehydrogenase I determines the specificity for coenzyme
    BIOCHEMISTRY, Vol. 30, No. 26. (1991), pp. 6397-6401.
    by F Fan, JA Lorenzen, BV Plapp
    posted to ctbp nadp protein_sequence by barry to the group structural_bioinformatics on 2006-08-15 20:06:56 as * along with 1 group Bioinformatics
  • Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved.
    Structure, Vol. 13, No. 4. (April 2005), pp. 565-577.
    by W Zheng, BR Brooks, S Doniach, D Thirumalai
    posted to nma protein_dynamics protein_sequence protein_structure by barry to the group structural_bioinformatics on 2006-08-15 19:16:49 as * along with 1 group Bioinformatics
  • Crystal structure of a NAD-dependent D-glycerate dehydrogenase at 2.4 A resolution.
    J Mol Biol, Vol. 236, No. 4. (4 March 1994), pp. 1123-1140.
    by JD Goldberg, T Yoshida, P Brick
    posted to ctbp gdh by barry to the group structural_bioinformatics on 2006-08-09 22:27:38 as * along with 1 group Bioinformatics
  • Net, a negative Ras-switchable TCF, contains a second inhibition domain, the CID, that mediates repression through interactions with CtBP and de-acetylation.
    EMBO J, Vol. 18, No. 12. (15 June 1999), pp. 3392-3403.
    by P Criqui-Filipe, C Ducret, SM Maira, B Wasylyk
    posted to ctbp by barry to the group structural_bioinformatics on 2006-08-09 21:25:32 as * along with 1 group Bioinformatics
  • Interaction of the mitotic kinesin Eg5 inhibitor monastrol with P-glycoprotein
    Naunyn-Schmiedeberg's Archives Of Pharmacology, Vol. 372, No. 4. (January 2006), pp. 291-299.
    by Tanja Peters, Heike Lindenmaier, Walter E Haefeli, Johanna Weiss
    posted to drug_design eg5 kinesin molecular_motors monastrol by barry to the group structural_bioinformatics on 2006-07-24 18:50:31 as * along with 1 group Bioinformatics
  • Dynamical properties of fasciculin-2
    Proteins: Structure, Function, and Genetics, Vol. 36, No. 4. (1999), pp. 447-453.
    by Nathan A Baker, Volkhard Helms, Andrew J Mccammon
    posted to md_simulation protein_dynamics protein_structure by barry to the group structural_bioinformatics on 2006-07-22 18:38:37 as * along with 1 group Bioinformatics
  • The sliding filament model: 1972-2004.
    J Gen Physiol, Vol. 123, No. 6. (June 2004), pp. 643-656.
    by R Cooke
    posted to molecular_motors motor_model review by barry to the group structural_bioinformatics on 2006-05-11 19:21:06 as * along with 1 group Bioinformatics
  • Molecular determinants of gating at the potassium-channel selectivity filter
    Nature Structural & Molecular Biology, Vol. 13, No. 4. (12 March 2006), pp. 311-318.
    by Julio F Cordero-Morales, Luis G Cuello, Yanxiang Zhao, Vishwanath Jogini, Marien D Cortes, Benoît Roux, Eduardo Perozo
    posted to ion_channels ksca by barry to the group structural_bioinformatics on 2006-04-06 18:27:06 as * along with 1 group Bioinformatics
  • Molecular Dynamics Simulations of the Complete Satellite Tobacco Mosaic Virus
    Structure, Vol. 14, No. 3. (March 2006), pp. 437-449.
    by Peter L Freddolino, Anton S Arkhipov, Steven B Larson, Alexander Mcpherson, Klaus Schulten
    posted to md_simulation protein_structure by barry to the group structural_bioinformatics on 2006-03-15 07:47:21 as * along with 1 person and 1 group RamuAnandakrishnan Bioinformatics
  • Pairwise protein structure alignment based on an orientation-independent backbone representation.
    J Bioinform Comput Biol, Vol. 2, No. 4. (December 2004), pp. 699-717.
    by J Ye, R Janardan, S Liu
    posted to bioinf_methods protein_structure structural_bioinformatics structure_comparison by barry to the group structural_bioinformatics on 2006-01-25 03:30:29 as * along with 1 group Bioinformatics
  • A tutorial of recent developments in the seeding of local alignment.
    J Bioinform Comput Biol, Vol. 2, No. 4. (December 2004), pp. 819-842.
    by DG Brown, M Li, B Ma
    posted to bioinf_methods protein_sequence sequence_comparison by barry to the group structural_bioinformatics on 2006-01-25 03:04:09 as * along with 1 person and 1 group nedwards Bioinformatics
  • wafr.pdf (application/pdf Object)
    by Lotan, Latombe
    posted to bioinf_methods loop_modeling protein_structure by barry to the group structural_bioinformatics on 2006-01-09 18:40:42 as * along with 1 person and 1 group apaydin Bioinformatics
  • Cytoplasmic microtubule-based motor proteins
    Current Opinion in Cell Biology, Vol. 5, No. 1. (February 1993), pp. 95-104.
    by Dimitrios A Skoufias, Jonathan M Scholey
    posted to dynein kinesin molecular_motors review by barry to the group structural_bioinformatics on 2006-01-09 18:11:49 as * along with 1 group Bioinformatics
  • A Pathway for the Transmission of Allosteric Signals in the Ribosome through a Network of RNA Tertiary Interactions
    Journal of Molecular Biology, Vol. 355, No. 5. (3 February 2006), pp. 1014-1025.
    by Yuen-Ling Chan, John Dresios, Ira G Wool
    posted to allosteric ribosome by barry to the group structural_bioinformatics on 2006-01-02 19:17:14 as * along with 1 group Bioinformatics
  • Model for kinetics of wild-type and mutant kinesins.
    Biosystems (22 December 2005)
    by Ping Xie, Shuo-Xing X Dou, Peng-Ye Y Wang
    posted to kinesin molecular_motors motor_model by barry to the group structural_bioinformatics on 2006-01-02 19:08:48 as * along with 2 people and 1 group shuns qwermish Bioinformatics
  • A method for including protein flexibility in protein-ligand docking: improving tools for database mining and virtual screening
    Journal of Molecular Graphics and Modelling, Vol. 18, No. 3. (June 2000), pp. 247-257.
    by Howard B Broughton
    posted to bioinformatics general test by barry to the group structural_bioinformatics on 2005-12-16 16:17:25 as * along with 1 group Bioinformatics
  • What Limits the Velocity of Fast-skeletal Muscle Contraction in Mammals?
    Journal of Molecular Biology, Vol. 355, No. 3. (20 January 2006), pp. 432-442.
    by Miklos Nyitrai, Rosetta Rossi, Nancy Adamek, Maria A Pellegrino, Roberto Bottinelli, Michael A Geeves
    posted to molecular_motors myosin by barry to the group structural_bioinformatics on 2005-12-15 12:22:54 as * along with 1 person and 1 group shuns Bioinformatics
  • Cooperative cargo transport by several molecular motors
    Proceedings Of The National Academy Of Sciences Of The United States Of America, Vol. 102, No. 48. (29 November 2005), pp. 17284-17289.
    by Stefan Klumpp, Reinhard Lipowsky
    posted to molecular_motors motor_model by barry to the group structural_bioinformatics on 2005-12-05 19:22:32 as * along with 1 group Bioinformatics
  • Comparative molecular dynamics--similar folds and similar motions?
    Proteins, Vol. 61, No. 4. (1 December 2005), pp. 809-822.
    by Andrew Pang, Yalini Arinaminpathy, Mark S Sansom, Philip C Biggin
    posted to md_simulation structural_bioinformatics structure_comparison by barry to the group structural_bioinformatics on 2005-11-29 23:22:16 as * along with 1 group Bioinformatics
  • ROCR: visualizing classifier performance in R
    Bioinformatics, Vol. 21, No. 20. (15 October 2005), pp. 3940-3941.
    by Tobias Sing, Oliver Sander, Niko Beerenwinkel, Thomas Lengauer
    posted to statistics by ana to the group structural_bioinformatics on 2005-11-29 22:16:39 as * along with 3 people and 1 group balajis chad_davis baldigroup Bioinformatics
  • Ligand binding affinities from MD simulations.
    Acc Chem Res, Vol. 35, No. 6. (June 2002), pp. 358-365.
    by J Aqvist, VB Luzhkov, BO Brandsdal
    posted to free_energy md_simulation by barry to the group structural_bioinformatics on 2005-10-26 00:14:13 as * along with 3 people and 1 group baaden dimka superpyrin Bioinformatics
  • Intraflagellar Transport: Keeping the Motors Coordinated
    Current Biology, Vol. 15, No. 19. (11 October 2005), pp. R798-R801.
    by Douglas G Cole
    posted to molecular_motors review by barry to the group structural_bioinformatics on 2005-10-12 23:57:19 as * along with 1 group Bioinformatics
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