registrieren | anmelden | FAQ      [?] 
Recent | Unread | Search | Authors | Tags | Export

hmks library [102 articles]

Neue Artikel in hmks Bibliothek.
  • Protein Side-Chain Placement Through MAP Estimation and Problem-Size Reduction,
    pp. 219-230.
    posted to side_chain_prediction protein_structure protein_design inference graphical_models by hmk on 2008-07-20 15:54:09 as **
  • Thermodynamic basis of resistance to HIV-1 protease inhibition: calorimetric analysis of the V82F/I84V active site resistant mutant.
    Biochemistry, Vol. 39, No. 39. (3 October 2000), pp. 11876-11883.
    by MJ Todd, I Luque, A Velázquez-Campoy, E Freire
    posted to protein_structure hivpr drug_design data alternatives by hmk on 2008-07-08 15:27:35 as **
  • Kinetic characterization and cross-resistance patterns of HIV-1 protease mutants selected under drug pressure.
    Biochemistry, Vol. 34, No. 29. (25 July 1995), pp. 9282-9287.
    by SV Gulnik, LI Suvorov, B Liu, B Yu, B Anderson, H Mitsuya, JW Erickson
    posted to protein_structure hivpr drug_design data by hmk on 2008-07-08 15:25:51 as **
  • A simple physical model for binding energy hot spots in protein-protein complexes.
    Proc Natl Acad Sci U S A, Vol. 99, No. 22. (29 October 2002), pp. 14116-14121.
    by T Kortemme, D Baker
    posted to protein_protein_interactions molecular_mechanics free_energy data alternatives by hmk on 2008-06-01 00:24:36 as ** along with 5 people and 1 group skoddet lna jwm bicko cjeans Nielsen group
  • Unified approach for molecular dynamics and density-functional theory
    Physical Review Letters, Vol. 55 (November 1985), pp. 2471-2474.
    by R Car, M Parrinello
    posted to free_energy molecular_dynamics physics quantum_physics by hmk on 2008-04-10 07:07:29 as ** along with 2 people and_ped10 eyliu
  • "Mining Minima": Direct Computation of Conformational Free Energy
    J. Phys. Chem. A, Vol. 101, No. 8. (20 February 1997), pp. 1609-1618.
    by MS Head, JA Given, MK Gilson
    posted to free_energy by hmk on 2008-04-03 20:52:59 as **
  • Calculation of protein-ligand binding affinities.
    Annu Rev Biophys Biomol Struct, Vol. 36 (2007), pp. 21-42.
    by MK Gilson, HX Zhou
    posted to alternatives binding data free_energy by hmk on 2008-04-03 20:50:50 as ** along with 5 people and 1 group cchang ras dimka neils ashaytan group
  • Extraction of configurational entropy from molecular simulations via an expansion approximation
    The Journal of Chemical Physics, Vol. 127, No. 2. (2007)
    by Benjamin J Killian, Joslyn Y Kravitz, Michael K Gilson
    posted to free_energy protein_structure by hmk on 2008-04-03 20:46:55 as **
  • A new class of models for computing receptor-ligand binding affinities
    Chemistry & Biology, Vol. 4, No. 2. (1997), pp. 87-92.
    by Michael K Gilson, James A Given, Martha S Head
    posted to free_energy molecular_dynamics protein_protein_interactions by hmk on 2008-04-03 20:40:59 as **
  • The statistical-thermodynamic basis for computation of binding affinities: a critical review.
    Biophys J, Vol. 72, No. 3. (March 1997), pp. 1047-1069.
    by MK Gilson, JA Given, BL Bush, JA McCammon
    posted to entropy free_energy molecular_dynamics physics protein_structure review by hmk on 2008-04-03 20:07:07 as ** along with 2 people and 2 groups cchang ssomani group structure-bii
  • Spotlight: Computational Biology at the Beginning of the Post-genomic Era Thomas Lengauer
    posted to challenges free_energy by hmk on 2008-04-03 20:06:14 as **
  • Calculation of the Entropy and Free Energy from Monte Carlo Simulations of a Peptide Stretched by an External Force
    J. Phys. Chem. B, Vol. 109, No. 46. (24 November 2005), pp. 21963-21970.
    by S Cheluvaraja, H Meirovitch
    posted to data entropy free_energy molecular_dynamics protein_structure by hmk on 2008-04-03 19:54:33 as **
  • The atomic structure of protein-protein recognition sites
    Journal of Molecular Biology, Vol. 285, No. 5. (5 February 1999), pp. 2177-2198.
    by Loredana L Conte, Cyrus Chothia, Joel Janin
    posted to data free_energy graphical_models protein_protein_interactions by hmk on 2008-03-15 22:31:01 as **
  • On Design of Optimal Nonlinear Kernel Potential Function for Protein Folding and Protein Design
    by Changyu Hu, Xiang Li, Jie Liang
    posted to data decoy decoy_detection molecular_mechanics protein_design protein_structure by hmk on 2008-01-06 00:26:29 as **
  • Framework for kernel regularization with application to protein clustering
    Proceedings of the National Academy of Sciences, Vol. 102, No. 35. (30 August 2005), pp. 12332-12337.
    by Fan Lu, Sunduz Keles, Stephen J Wright, Grace Wahba
    posted to alternatives data dynamics molecular_dynamics protein_structure by hmk on 2007-12-25 01:10:04 as **
  • Can a physics-based, all-atom potential find a protein's native structure among misfolded structures? I. Large scale AMBER benchmarking
    Journal of Computational Chemistry, Vol. 28, No. 12. (2007), pp. 2059-2066.
    by Liliana Wroblewska, Jeffrey Skolnick
    posted to alternatives data decoy decoy_detection free_energy molecular_dynamics by hmk on 2007-12-12 16:49:46 as ** along with 1 person pawelp
  • Computational design of protein-protein interactions.
    Curr Opin Chem Biol, Vol. 8, No. 1. (February 2004), pp. 91-97.
    by T Kortemme, D Baker
    posted to alternatives data molecular_mechanics physics protein_protein_interactions by hmk on 2007-12-12 15:44:14 as ** along with 5 people jteyra lna jwm bicko cjeans
  • A consensus view of fold space: combining SCOP, CATH, and the Dali Domain Dictionary.
    Protein Sci, Vol. 12, No. 10. (October 2003), pp. 2150-2160.
    by R Day, DA Beck, RS Armen, V Daggett
    posted to data protein_fold protein_structure by hmk on 2007-12-09 05:38:39 as ** along with 4 people and 2 groups ana barry tjimenez dimka structural_bioinformatics Bioinformatics
  • Ensemble versus single-molecule protein unfolding.
    Proc Natl Acad Sci U S A, Vol. 102, No. 38. (20 September 2005), pp. 13445-13450.
    by R Day, V Daggett
    posted to data ensemble molecular_dynamics by hmk on 2007-12-09 05:25:34 as ** along with 2 people bilab choonpeng
  • Wordom: a program for efficient analysis of molecular dynamics simulations
    Bioinformatics, Vol. 23, No. 19. (1 October 2007), pp. 2625-2627.
    by Michele Seeber, Marco Cecchini, Francesco Rao, Giovanni Settanni, Amedeo Caflisch
    posted to alternatives molecular_dynamics protein_folding by hmk on 2007-12-09 05:02:58 as ** along with 6 people and 2 groups jyuh barry tmmurali choonpeng sobolevnrm LamBras structural_bioinformatics baker-group
  • Coarse-Grained Biomolecular Simulation with REACH: Realistic Extension Algorithm via Covariance Hessian
    Biophys. J., Vol. 93, No. 10. (15 November 2007), pp. 3460-3469.
    by Kei Moritsugu, Jeremy C Smith
    posted to alternatives graphical_models molecular_dynamics protein_folding by hmk on 2007-12-09 03:09:17 as ** along with 2 people and 1 group aqeel sobolevnrm baker-group
  • High-throughput modeling and analysis of protein structural dynamics
    Brief Bioinform, Vol. 8, No. 6. (1 November 2007), pp. 432-445.
    by Xiong Liu, Hassan A Karimi
    posted to alternatives data molecular_dynamics protein_structure by hmk on 2007-12-09 02:50:59 as ** along with 1 person aqeel
  • A consensus view of protein dynamics.
    Proc Natl Acad Sci U S A (10 January 2007)
    by Manuel Rueda, Carles Ferrer-Costa, Tim Meyer, Alberto Pérez, Jordi Camps, Adam Hospital, Josep Lluis L Gelpí, Modesto Orozco
    posted to data dynamics graphical_models molecular_dynamics by hmk on 2007-12-09 02:49:20 as ** along with 12 people and 2 groups LamBras lna dimka aqeel aswin rabio grahamc zwang biehl Ema phoenixzxl ras ParkinsonLab_at_MaRS The BMM Dome
  • Information Theory and Statistical Mechanics
    Physical Review, Vol. 106, No. 4. (15 May 1957), 620.
    by ET Jaynes
    posted to inference information_theory molecular_mechanics statistics by hmk on 2007-12-07 06:41:06 as ** along with 5 people varung dcoates ddahlem nathanielvirgo jenda_z
  • Single-Molecule Dynamics Reveals Cooperative Binding-Folding in Protein Recognition
    PLoS Computational Biology, Vol. 2, No. 7. (1 July 2006), e78.
    by Jin Wang, Qiang Lu, Peter H Lu
    posted to dynamics molecular_dynamics by hmk on 2007-12-07 03:51:09 as **
  • Construction of effective free energy landscape from single-molecule time series
    Proceedings of the National Academy of Sciences, Vol. 104, No. 49. (4 December 2007), pp. 19297-19302.
    by Akinori Baba, Tamiki Komatsuzaki
    posted to free_energy graphical_models protein_folding protein_structure by hmk on 2007-12-07 03:49:47 as ** along with 6 people and 1 group hsekiguc zwang cactus sobolevnrm Diego_Prada arnaudriegert baker-group
  • Protein Free Energy Landscapes Remodeled by Ligand Binding
    Biophys. J., Vol. 93, No. 2. (15 July 2007), pp. 579-585.
    by Troy C Messina, David S Talaga
    posted to free_energy graphical_models protein_folding protein_structure by hmk on 2007-12-07 03:46:10 as **
  • Large-scale characteristics of the energy landscape in protein-protein interactions.
    Proteins (11 October 2007)
    by Nicholas O'toole, Ilya A A Vakser
    posted to free_energy protein_folding protein_protein_interactions protein_structure by hmk on 2007-12-06 07:18:22 as ** along with 2 people bicko paulschlesinger
  • Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction
    PNAS, Vol. 103, No. 26. (27 June 2006), pp. 9885-9890.
    by Payel Das, Mark Moll, Hernan Stamati, Lydia E Kavraki, Cecilia Clementi
    posted to dynamics free_energy graphical_models protein_folding by hmk on 2007-12-06 00:10:32 as ** along with 2 people and 2 groups samjlord sobolevnrm moernerlab baker-group
  • Sampling Realistic Protein Conformations Using Local Structural Bias.
    PLoS Comput Biol, Vol. 2, No. 9. (22 September 2006)
    by Thomas Hamelryck, John T T Kent, Anders Krogh
    posted to free_energy graphical_models protein_fold protein_structure statistics by hmk on 2007-10-31 17:54:26 as ***** along with 2 people wouterboomsma j3xucite
  • Computational design of antibody-affinity improvement beyond in vivo maturation.
    Nat Biotechnol (23 September 2007)
    by Shaun M M Lippow, K Dane D Wittrup, Bruce Tidor
    posted to data free_energy graphical_models protein_design protein_fold protein_structure by hmk on 2007-10-31 14:06:33 as ***** along with 1 person and 1 group zwang group
  • Toward high-resolution prediction and design of transmembrane helical protein structures
    Proceedings of the National Academy of Sciences, Vol. 104, No. 40. (2 October 2007), pp. 15682-15687.
    by P Barth, J Schonbrun, D Baker
    posted to data decoy_detection molecular_mechanics physics protein_structure by hmk on 2007-10-02 22:57:07 as ** along with 3 people zwang biehl Ema
  • Clinical forecasting in drug development
    Nature Reviews Drug Discovery, Vol. 6, No. 2., pp. 107-108.
    by Asher D Schachter, Marco F Ramoni
    posted to graphical_models industry pharma by hmk on 2007-06-09 19:15:23 as **
  • Ten Simple Rules for Making Good Oral Presentations
    PLoS Computational Biology, Vol. 3, No. 4. (1 April 2007), e77.
    by Philip E Bourne
    posted to advice by hmk on 2007-05-07 17:18:14 as ** along with 7 people and 1 group bxk jfr Yanno timflutre rodney zwang Torsten_Holmer Kopelman_Group
  • Recognition of errors in three-dimensional structures of proteins.
    Proteins, Vol. 17, No. 4. (December 1993), pp. 355-362.
    by MJ Sippl
    posted to decoy_detection free_energy graphical_models by hmk on 2007-04-28 23:50:26 as ** along with 1 person chad_davis
  • All are not equal: A benchmark of different homology modeling programs
    Protein Sci, Vol. 14, No. 5. (1 May 2005), pp. 1315-1327.
    by Bjorn Wallner, Arne Elofsson
    posted to protein_structure side_chain_prediction by hmk on 2007-04-10 21:39:25 as ** along with 5 people and 2 groups karbak marcius eweaver BioNica rsantana BioinfoCIPF SGU-CIPF
  • Diverse, high-quality test set for the validation of protein-ligand docking performance.
    J Med Chem, Vol. 50, No. 4. (22 February 2007), pp. 726-741.
    by MJ Hartshorn, ML Verdonk, G Chessari, SC Brewerton, WT Mooij, PN Mortenson, CW Murray
    posted to data decoy_detection docking by hmk on 2007-03-30 17:55:36 as ** along with 5 people thanatos BragilMassoud daevans ramensky superpyrin
  • Modeling protein conformational ensembles: From missing loops to equilibrium fluctuations
    Proteins: Structure, Function, and Bioinformatics, Vol. 65, No. 1. (2006), pp. 164-179.
    by Amarda Shehu, Cecilia Clementi, Lydia E Kavraki
    posted to free_energy loops protein_structure by hmk on 2007-03-23 01:39:24 as ** along with 6 people and 2 groups apaydin nigham aqeel yongzhao elham sobolevnrm TSRI_MGL baker-group
  • An Orientation-dependent Hydrogen Bonding Potential Improves Prediction of Specificity and Structure for Proteins and Protein-Protein Complexes
    Journal of Molecular Biology, Vol. 326, No. 4. (28 February 2003), pp. 1239-1259.
    by Tanja Kortemme, Alexandre V Morozov, David Baker
    posted to molecular_mechanics physics protein_structure side_chain_prediction by hmk on 2007-03-15 20:47:05 as ** along with 1 person mirzazadeh
  • Design of a novel globular protein fold with atomic-level accuracy.
    Science, Vol. 302, No. 5649. (21 November 2003), pp. 1364-1368.
    by B Kuhlman, G Dantas, GC Ireton, G Varani, BL Stoddard, D Baker
    posted to graphical_models molecular_mechanics physics protein_structure by hmk on 2007-03-14 01:23:38 as ** along with 5 people ca3295 jwm chad_davis heymiki kevinchannon
  • Effective energy function for proteins in solution.
    Proteins, Vol. 35, No. 2. (1 May 1999), pp. 133-152.
    by T Lazaridis, M Karplus
    posted to molecular_mechanics physics protein_structure by hmk on 2007-03-13 18:18:43 as ** along with 4 people and 2 groups kgutwin marcius bluvsh1 choonpeng BioinfoCIPF SGU-CIPF
  • A bird's eye view of density functional theory
    by Klaus Capelle
    posted to physics by hmk on 2007-03-12 05:10:53 as **
  • Structural stability of oligomeric proteins: A mean-field theoretical approach
    Journal of Computer-Aided Materials Design, Vol. V4, No. 1. (1 April 1997), pp. 1-8.
    by Armin R Vã¶lkel, Jaan Noolandi
    posted to free_energy inference protein_structure by hmk on 2007-03-09 00:04:55 as **
  • Streptavidin Tetramerization and 2D Crystallization: A Mean-Field Approach
    Biophys. J., Vol. 80, No. 4. (1 April 2001), pp. 2004-2010.
    by T Coussaert, AR Volkel, J Noolandi, AP Gast
    posted to free_energy graphical_models inference protein_structure by hmk on 2007-03-09 00:01:52 as **
  • The Cluster Variation Method for Efficient Linkage Analysis on Extended Pedigrees
    BMC Bioinformatics, Vol. 7, No. Suppl 1. (2006)
    by Cornelis Albers, Martijn Leisink, Hilbert Kappen
    posted to free_energy graphical_models by hmk on 2007-03-07 02:40:46 as **
  • Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions.
    J Mol Biol, Vol. 268, No. 1. (25 April 1997), pp. 209-225.
    by KT Simons, C Kooperberg, E Huang, D Baker
    posted to decoy_detection protein_structure by hmk on 2007-03-03 20:47:53 as ** along with 7 people and 2 groups joule ana jwm vavi wouterboomsma j3xucite mijam structural_bioinformatics Bioinformatics
  • Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins
    Proteins: Structure, Function, and Genetics, Vol. 34, No. 1., pp. 82-95.
    by Kim T Simons, Ingo Ruczinski, Charles Kooperberg, Brian A Fox, Chris Bystroff, David Baker
    posted to decoy_detection protein_structure by hmk on 2007-03-03 20:45:55 as ** along with 1 person bpb
  • Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations.
    J Mol Biol, Vol. 331, No. 1. (1 August 2003), pp. 281-299.
    by JJ Gray, S Moughon, C Wang, O Schueler-Furman, B Kuhlman, CA Rohl, D Baker
    posted to data decoy_detection docking protein_structure by hmk on 2007-03-02 22:35:12 as ** along with 1 person jwm
  • Improved side-chain modeling for protein-protein docking.
    Protein Sci, Vol. 14, No. 5. (May 2005), pp. 1328-1339.
    by C Wang, O Schueler-Furman, D Baker
    posted to decoy_detection docking protein_structure by hmk on 2007-03-02 22:33:34 as ** along with 9 people and 3 groups barry aqeel jwm bicko yongzhao blackbart bluvsh1 selrac Evangelia structural_bioinformatics Bioinformatics TSRI_MGL
  • Influence of protein structure databases on the predictive power of statistical pair potentials
    Proteins: Structure, Function, and Genetics, Vol. 31, No. 2. (1998), pp. 139-149.
    by Emiko Furuichi, Patrice Koehl
    posted to decoy_detection protein_structure by hmk on 2007-02-27 22:16:10 as **
    • Bemerkung: Sie können diese Seite wie folgt zitieren: http://www.citeulike.org/user/hmk

    Result page: 1 2 Next RIS BibTeX RSS
    CiteULike organises scholarly (or academic) papers or literature and provides bibliographic (which means it makes bibliographies) for universities and higher education establishments. It helps undergraduates and postgraduates. People studying for PhDs or in postdoctoral (postdoc) positions. The service is similar in scope to EndNote or RefWorks or any other reference manager like BibTeX, but it is a social bookmarking service for scientists and humanities researchers.