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Group: structural_bioinformatics - library [1338 articles]

Neue Artikel von Mitliedern der Gruppe structural_bioinformatics Gruppe
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  • ANGLOR: A Composite Machine-Learning Algorithm for Protein Backbone Torsion Angle Prediction
    PLoS ONE, Vol. 3, No. 10. (15 October 2008), e3400.
    by Sitao Wu, Yang Zhang
    posted to pb by svozil to the group structural_bioinformatics on 2008-12-31 13:50:59 as ***** along with 1 group Bioinformatics
  • Conformer Selection and Induced Fit in Flexible Backbone Protein–Protein Docking Using Computational and NMR Ensembles
    Journal of Molecular Biology, Vol. 381, No. 4. (12 September 2008), pp. 1068-1087.
    by S Chaudhury, J Gray
    posted to protein_protein docking conformational_selection by barry to the group structural_bioinformatics on 2008-12-02 18:12:27 as ** along with 1 group McCammon
  • 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
  • Principles of flexible protein-protein docking
    Proteins: Structure, Function, and Bioinformatics, Vol. 73, No. 2. (2008), pp. 271-289.
    by Nelly Andrusier, Efrat Mashiach, Ruth Nussinov, Haim J Wolfson
    posted to review protein flexible docking by csrocha to the group structural_bioinformatics on 2008-11-10 18:05:05 as ** along with 2 people aqeel LamBras
  • Structural insights into G-protein-coupled receptor activation.
    Current opinion in structural biology (25 October 2008)
    by William I I Weis, Brian K K Kobilka
    posted to review gpcr by barry to the group structural_bioinformatics on 2008-11-07 01:19:41 as ** along with 1 group McCammon
  • notes Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web
    PLoS Comput Biol, Vol. 4, No. 10. (31 October 2008), e1000204.
    by Duncan Hull, Steve R Pettifer, Douglas B Kell
    posted to review data_integration classic by chad_davis to the group structural_bioinformatics on 2008-10-31 08:58:42 as ***** along with 81 people and 7 groups Koh OriginalLurch sototozo akraemer thegoose kharke niallhaslam rdmagnuson JuanGiarrizzo pkonings jennialp lgibson rmasur GJNauta puchu rrbarb amarois mneeley dr_lee_xray IRTADOC zilvlan curthh mount_misery narroyo rdiaz treangen hpaces bumatic BerndBerndsen esterhasz phreeza dbk rempeljl teachingaging cs02 joseph_x_zhou continea Rosetta fletchad Betelgeuse60 tomroper 1971biblio timrwatkins rschulz cisevol ryan smithrise silberbauer natstreet pick600 xjlibod ukppdadsr robertlischke bookwormzz NIlz junwang4 taguchi tag barry kristgy caseybrown Gaetan bcondon lynnefox marekrud nuin sdgsilvana ckai1 guhjy neils carlfulp norris jago druvus alhoori emayorga GeeSharpMinor fgibson Zephyrus leonardo dullhunk MEHTRadiology Département Hypermédia - Master NET JacksonLab BergmanLab McCammon kpa-resources Roswell Cancer Crosstalk
  • Principal component analysis for protein folding dynamics
    Journal of Molecular Biology (15 October 2008)
    by G Maisuradze, A Liwo, H Scheraga
    posted to protein_folding pca by barry to the group structural_bioinformatics on 2008-10-30 04:05:03 as ** along with 2 people phoenixzxl paulschlesinger
  • Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms
    Proceedings of the National Academy of Sciences, Vol. 105, No. 32. (2008), pp. 11182-11187.
    by Kei-Ichi Okazaki, Shoji Takada
    posted to protein_dynamics allosteric by barry to the group structural_bioinformatics on 2008-10-27 22:23:54 as ** along with 3 people and 1 group raik ruvido zwang McCammon
  • 2D depiction of nonbonding interactions for protein complexes.
    Journal of computational chemistry (22 October 2008)
    by Peng Zhou, Feifei Tian, Zhicai Shang
    posted to protein_protein bioinf_methods by barry to the group structural_bioinformatics on 2008-10-25 17:59:23 as ** along with 1 person and 1 group higueruelo 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 **
  • Small and large scale conformational changes of adenylate kinase: a molecular dynamics study of the subdomain motion and mechanics.
    Biophysical journal (17 October 2008)
    by Francesco Pontiggia, Andrea Zen, Cristian Micheletti
    posted to md_simulation conformational_selection adk by barry to the group structural_bioinformatics on 2008-10-23 12:23:59 as ** along with 1 group McCammon
  • Pore loops of the AAA+ ClpX machine grip substrates to drive translocation and unfolding.
    Nature structural & molecular biology (19 October 2008)
    by Andreas Martin, Tania A A Baker, Robert T T Sauer
    posted to clipx aaa by barry to the group structural_bioinformatics on 2008-10-23 12:18:10 as ** along with 1 group McCammon
  • Finding and characterizing tunnels in macromolecules with application to ion channels and pores
    Biophys. J. (10 October 2008), biophysj.108.135970.
    by Ryan G Coleman, Kim A Sharp
    posted to ion_channels bioinf_methods by barry to the group structural_bioinformatics on 2008-10-18 09:41:33 as ** along with 1 person paulschlesinger
  • 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
  • Protein Crystallography (Molecular Biology Series)
    (28 January 1976)
    by TL Blundell, Lewis Johnson
    posted to protein crystallography by csrocha to the group structural_bioinformatics on 2008-10-17 19:18:39 as *
  • Surface Sites for Engineering Allosteric Control in Proteins
    Science, Vol. 322, No. 5900. (17 October 2008), pp. 438-442.
    by Jeeyeon Lee, Madhusudan Natarajan, Vishal C Nashine, Michael Socolich, Tina Vo, William P Russ, Stephen J Benkovic, Rama Ranganathan
    posted to sca protein_design correlated_mutations allosteric by barry to the group structural_bioinformatics on 2008-10-17 03:06:04 as *** along with 6 people and 2 groups jbhiatt lflorez cactus marck i000 paulschlesinger McCammon Bioinformatics
  • Protein docking using spherical polar Fourier correlations.
    Proteins, Vol. 39, No. 2. (1 May 2000), pp. 178-194.
    by DW Ritchie, GJ Kemp
    posted to spherical shape protein polar harmonics fourier electrostatic docking correlation complementary by csrocha to the group structural_bioinformatics on 2008-10-13 14:22:43 as ** along with 3 people martainn tjimenez bicko
  • Native state proline isomerization: an intrinsic molecular switch.
    Biochemistry, Vol. 42, No. 32. (19 August 2003), pp. 9515-9524.
    by AH Andreotti
    posted to review proline cis_trans by barry to the group structural_bioinformatics on 2008-10-11 04:47:18 as **
  • Docking and scoring protein complexes: CAPRI 3rd Edition
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Marc F Lensink, Raúl Méndez, Shoshana J Wodak
    posted to docking capri benchmark by csrocha to the group structural_bioinformatics on 2008-10-10 15:14:58 as ** along with 7 people bicko ruvido cjeans carlescorbi yalexeev middledomain timg
  • Normal modes and essential dynamics.
    Methods in molecular biology (Clifton, N.J.), Vol. 443 (2008), pp. 89-106.
    by S Hayward, BL de Groot
    posted to protein normal modes dynamic by csrocha to the group structural_bioinformatics on 2008-10-10 15:08:02 as ** along with 3 people ruvido LamBras higueruelo
  • Prediction of protein-protein interactions: the CAPRI experiment, its evaluation and implications.
    Curr Opin Struct Biol, Vol. 14, No. 2. (April 2004), pp. 242-249.
    by SJ Wodak, R Méndez
    posted to protein prediction interaction docking capri biological by csrocha to the group structural_bioinformatics on 2008-10-08 05:42:28 as ** along with 3 people nachtalp ffranca ruvido
  • Prediction of physical protein–protein interactions
    Physical Biology, Vol. 2, No. 2. (June 2005), S1.
    by András Szilágyi, Vera Grimm, Adrián K Arakaki, Jeffrey Skolnick
    posted to protein prediction docking by csrocha to the group structural_bioinformatics on 2008-10-08 05:34:01 as ** along with 2 people and 1 group lfriedl ruvido kdl
  • Dissecting protein-protein recognition sites
    Proteins: Structure, Function, and Genetics, Vol. 47, No. 3. (2002), pp. 334-343.
    by Pinak Chakrabarti, Joël Janin
    posted to protein interface docking biological by csrocha to the group structural_bioinformatics on 2008-10-08 04:34:14 as ** along with 1 person dfgreen
  • 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
  • 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 structural_bioinformatics on 2008-10-05 19:05:40 as ** along with 6 people and 4 groups sobolevnrm aqeel apaydin ruvido agrossfield skoddet baker-group Nielsen group McCammon 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 structural_bioinformatics on 2008-10-05 18:59:32 as * along with 2 people and 1 group mijam middledomain McCammon
  • 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 structural_bioinformatics on 2008-10-02 20:24:17 as ***** along with 5 people and 2 groups balicea grahamc fhsantanna marti sjcockell 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
  • 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 structural_bioinformatics on 2008-10-02 19:48:14 as ** along with 2 people and 2 groups oteri aqeel McCammon 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 structural_bioinformatics on 2008-10-02 19:46:30 as ** along with 3 people and 2 groups bpb zwang cmzmasek McCammon 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 structural_bioinformatics on 2008-10-02 19:21:02 as ** along with 2 people and 2 groups grahamc paulschlesinger 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
  • 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 structural_bioinformatics on 2008-09-30 18:44:35 as *** along with 5 people and 2 groups balicea grahamc markchen zwang cabbagesofdoom McCammon 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 structural_bioinformatics on 2008-09-29 01:52:45 as read along with 2 people and 2 groups martainn madhadron McCammon Bioinformatics
  • 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
  • Analyzing Protein Interaction Networks Using Structural Information
    Annual Review of Biochemistry, Vol. 77, No. 1. (2008)
    by Christina Kiel, Pedro Beltrao, Luis Serrano
    posted to structure review proj_interprets proj_assembly ppi networks embl data_integration by chad_davis to the group structural_bioinformatics on 2008-09-17 16:51:19 as *** along with 9 people kshameer Borelli bicko neils Evangelia grahamc paolomarcatili phoenixzxl zwang
  • Application of the level-set method to the implicit solvation of nonpolar molecules
    The Journal of Chemical Physics, Vol. 127, No. 8. (2007)
    by Li T Cheng, Joachim Dzubiella, Andrew J Mccammon, Bo Li
    posted to solvation set molecular level implicit by csrocha to the group structural_bioinformatics on 2008-09-15 15:06:32 as **** along with 1 person and 1 group sobolevnrm baker-group
  • Efficient molecular surface generation using level-set methods
    Journal of Molecular Graphics and Modelling, Vol. 25, No. 4. (December 2006), pp. 442-454.
    by Tolga Can, Chao-I Chen, Yuan-Fang Wang
    posted to surface sets molecular level by csrocha to the group structural_bioinformatics on 2008-09-15 15:01:21 as **
  • 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
  • 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
  • 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 structural_bioinformatics on 2008-08-29 19:08:02 as *** along with 1 person and 2 groups sobolevnrm baker-group McCammon
  • 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 structural_bioinformatics on 2008-08-29 19:03:07 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 *
  • 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 structural_bioinformatics on 2008-08-26 18:45:20 as ***** along with 2 groups Bioinformatics McCammon
  • 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 structural_bioinformatics on 2008-08-23 20:39:33 as ** along with 1 person and 1 group ruvido McCammon
  • Fast embedding methods for clustering tens of thousands of sequences.
    Computational biology and chemistry, Vol. 32, No. 4. (August 2008), pp. 282-286.
    by G Blackshields, M Larkin, IM Wallace, A Wilm, DG Higgins
    posted to bioinf_methods clustering protein_sequence by barry to the group structural_bioinformatics on 2008-08-23 20:27:35 as **** along with 1 group Bioinformatics
  • 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 17 people and 1 group antonkratz daforerog treangen natstreet nlapalu druvus jamselem dullhunk laughcry ibuch urgi sci91078 renatomilani xili03 phoenixzxl guhjy chad_davis Bioinformatics
  • 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 structural_bioinformatics on 2008-08-20 22:16:00 as ** along with 1 group McCammon
  • Extensive Conformational Transitions Are Required to Turn On ATP Hydrolysis in Myosin
    Journal of Molecular Biology, Vol. 381, No. 5. (19 September 2008), pp. 1407-1420.
    by Yang Yang, Haibo Yu, Qiang Cui
    posted to md_simulation molecular_motors motor_model myosin qm by barry to the group structural_bioinformatics on 2008-08-18 20:21:10 as ** along with 1 group Bioinformatics
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