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hmk's library [103 articles]

Recent papers added to hmk's library.
  • 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 7 people and 1 group qaiser_fatmi boris_aguilar 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 3 people and 1 group choonpeng 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 **
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