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Group: structural_bioinformatics - library [1321 articles]

グループ structural_bioinformatics のメンバーが最近追加した論文の一覧
  • 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 8 people bicko chad_davis 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 2 people 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 4 people nachtalp chad_davis 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 **
  • 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 2 people and 3 groups agrossfield skoddet 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 1 person and 1 group 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 1 person and 2 groups 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 2 people 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 1 person and 2 groups 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 1 person and 2 groups 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 1 person and 2 groups 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 1 person and 2 groups 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 6 people and 1 group 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 8 people 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 3 people and 2 groups chad_davis 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 11 people and 1 group jamselem dullhunk laughcry ibuch urgi sci91078 renatomilani xili03 phoenixzxl jyuh 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
  • 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
  • The importance of stupidity in scientific research
    J Cell Sci, Vol. 121, No. 11. (1 June 2008), 1771.
    by Martin A Schwartz
    posted to advice career essay by barry to the group structural_bioinformatics on 2008-07-16 22:25:46 as **** along with 6 people and 1 group aramata dullhunk arindrartow ibuch casutton jporternj 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 binding protein-protein titration by barry to the group structural_bioinformatics on 2008-07-08 01:26:01 as ** along with 5 people and 2 groups csrocha bicko chad_davis sobolevnrm RamuAnandakrishnan baker-group McCammon
  • X-ray structure of a prokaryotic pentameric ligand-gated ion channel
    Nature (05 March 2008)
    by Ricarda JC Hilf, Raimund Dutzler
    posted to achr ion_channel 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 md_simulation replica_exchange by barry to the group structural_bioinformatics on 2008-07-08 01:17:17 as ** along with 3 people and 2 groups agrossfield sobolevnrm loison baker-group McCammon
  • 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 drug_discovery protein_ligand 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 binding free_energy md_simulation protein-ligand by barry to the group structural_bioinformatics on 2008-07-08 01:12:03 as ** along with 3 people and 2 groups jmccammon biehl sobolevnrm baker-group McCammon
  • 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 free_energy md_simulation protein-ligand solvation by barry to the group structural_bioinformatics on 2008-07-08 01:11:30 as ** along with 2 people and 2 groups jmccammon sobolevnrm McCammon baker-group
  • 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 binding protein-protein by barry to the group structural_bioinformatics on 2008-07-08 00:52:29 as ** along with 4 people and 2 groups paulschlesinger higueruelo jmccammon cchang McCammon group
  • 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 person and 1 group RamuAnandakrishnan 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 coarse_grain replica_exchange by barry to the group structural_bioinformatics on 2008-07-08 00:49:57 as ** along with 3 people and 1 group RamuAnandakrishnan jmccammon zwang McCammon
  • 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
  • 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 algorithm alignment binding complexes data_integration modelling proj_assembly structure 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 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
  • 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 algorithm alignment complexes data_integration em modelling proj_assembly structure 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 algorithm binding complexes docking modelling proj_assembly structure 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 algorithm classification disorder ensemble proj_disocons structure by chad_davis to the group structural_bioinformatics on 2008-04-28 09:47:26 as ***** along with 1 person niallhaslam
    • 注: このページを引用する時は次のURLでどうぞ: http://www.citeulike.org/group/122

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