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ttjoseph library [84 articles]

Статьи, недавно добавленные в библиотеку ttjoseph .
  • Protein simulation below the glass-transition temperature. Dependence on cooling protocol
    Chemical Physics Letters, Vol. 226, No. 5-6. (26 August 1994), pp. 447-452.
    by Peter J Steinbach, Bernard R Brooks
    posted to molecular-dynamics simulated-annealing by ttjoseph on 2007-03-07 18:29:06 as **
  • All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
    J. Phys. Chem. B, Vol. 102, No. 18. (30 April 1998), pp. 3586-3616.
    by AD Mackerell, D Bashford, M Bellott, RL Dunbrack, JD Evanseck, MJ Field, S Fischer, J Gao, H Guo, S Ha, D Joseph-Mccarthy, L Kuchnir, K Kuczera, FTK Lau, C Mattos, S Michnick, T Ngo, DT Nguyen, B Prodhom, WE Reiher, B Roux, M Schlenkrich, JC Smith, R Stote, J Straub, M Watanabe, J Wiorkiewicz-Kuczera, D Yin, M Karplus
    posted to force-field molecular-dynamics by ttjoseph on 2007-03-07 04:39:41 as ** along with 4 people timg dimka papatonyhill ssomani
  • Automated docking of flexible ligands: Applications of autodock
    Journal of Molecular Recognition, Vol. 9, No. 1. (1996), pp. 1-5.
    by David S Goodsell, Garrett M Morris, Arthur J Olson
    posted to docking by ttjoseph on 2007-03-07 04:35:10 as **
  • New-Generation Amber United-Atom Force Field
    J. Phys. Chem. B, Vol. 110, No. 26. (6 July 2006), pp. 13166-13176.
    by L Yang, C Tan, MJ Hsieh, J Wang, Y Duan, P Cieplak, J Caldwell, PA Kollman, R Luo
    posted to force-field molecular-dynamics by ttjoseph on 2007-03-07 04:34:09 as **
  • Comparison of simple potential functions for simulating liquid water
    The Journal of Chemical Physics, Vol. 79, No. 2. (1983), pp. 926-935.
    by William L Jorgensen, Jayaraman Chandrasekhar, Jeffry D Madura, Roger W Impey, Michael L Klein
    posted to force-field molecular-dynamics by ttjoseph on 2007-03-07 04:08:15 as ** along with 8 people and 1 group mleis ffranca easybakemuffin ashaytan RamuAnandakrishnan r2s2 pavanghatty Diego_Prada CMB
  • Crystal Structures of RNase H Bound to an RNA/DNA Hybrid: Substrate Specificity and Metal-Dependent Catalysis
    Cell, Vol. 121, No. 7. (1 July 2005), pp. 1005-1016.
    by Marcin Nowotny, Sergei A Gaidamakov, Robert J Crouch, Wei Yang
    posted to cleavage crystal-structure rnase-h by ttjoseph on 2007-03-07 04:05:10 as ***
  • Steered molecular dynamics and mechanical functions of proteins
    Current Opinion in Structural Biology, Vol. 11, No. 2. (1 April 2001), pp. 224-230.
    by Barry Isralewitz, Mu Gao, Klaus Schulten
    posted to molecular-dynamics by ttjoseph on 2007-03-06 02:37:04 as ** along with 2 people and 2 groups barry LamBras structural_bioinformatics Bioinformatics
  • Simulated annealing with restrained molecular dynamics using a flexible restraint potential: Theory and evaluation with simulated NMR constraints
    Protein Sci, Vol. 5, No. 4. (1 April 1996), pp. 593-603.
    by D Bassolino-Klimas, R Tejero, SR Krystek, WJ Metzler, GT Montelione, RE Bruccoleri
    posted to molecular-dynamics simulated-annealing by ttjoseph on 2007-03-06 01:36:22 as ***
  • Scalable molecular dynamics with NAMD.
    J Comput Chem, Vol. 26, No. 16. (December 2005), pp. 1781-1802.
    by JC Phillips, R Braun, W Wang, J Gumbart, E Tajkhorshid, E Villa, C Chipot, RD Skeel, L Kalé, K Schulten
    posted to molecular-dynamics software by ttjoseph on 2007-03-02 16:13:33 as *** along with 10 people and 5 groups vahmurk gisle dimka jwm sangeetha yoel_rf bilab wilsoros sobolevnrm ibuch Radiation_Damage Stressosome Bioinformatics insilicodrug baker-group
  • Multi-Terminal Network Flows
    Journal of the Society for Industrial and Applied Mathematics, Vol. 9, No. 4. (1961), pp. 551-570.
    by RE Gomory, TC Hu
    posted to cs graph-theory by ttjoseph on 2007-03-02 03:33:12 as ***
  • Coarse-Graining in Polymer Simulation: From the Atomistic to the Mesoscopic Scale and Back
    ChemPhysChem, Vol. 3, No. 9. (2002), pp. 754-769.
    by Florian Müller-Plathe
    posted to coarse-graining simulation by ttjoseph on 2007-02-28 22:55:38 as ** along with 1 person kaz229
  • Graph Clustering and Minimum Cut Trees
    Internet Mathematics, Vol. 1, No. 4. (2004), pp. 385-408.
    by Gary W Flake, Robert E Tarjan, Kostas Tsioutsiouliklis
    posted to cs graph-theory by ttjoseph on 2007-02-22 02:11:06 as read along with 2 people rocarvaj AbnerCYH
  • Structure of the C-terminal half of UvrC reveals an RNase H endonuclease domain with an Argonaute-like catalytic triad.
    EMBO J, Vol. 26, No. 2. (24 January 2007), pp. 613-622.
    by E Karakas, JJ Truglio, D Croteau, B Rhau, L Wang, B Van Houten, C Kisker
    posted to argonaute by ttjoseph on 2007-01-30 00:49:06 as ***
  • Comparison of siRNA-induced off-target RNA and protein effects.
    RNA (19 January 2007)
    by Lourdes M M Alemán, John Doench, Phillip A A Sharp
    posted to sirna rnai by ttjoseph on 2007-01-30 00:48:38 as *** along with 1 person heliopais
  • Can Principal Components Yield a Dimension Reduced Description of Protein Dynamics on Long Time Scales?
    J. Phys. Chem. B, Vol. 110, No. 45. (16 November 2006), pp. 22842-22852.
    by OF Lange, H Grubmuller
    posted to molecular-dynamics essential-dynamics biophysics by ttjoseph on 2007-01-18 16:44:01 as *** along with 1 person ffranca
  • Stitching together RNA tertiary architectures
    Journal of Molecular Biology, Vol. 294, No. 4. (10 December 1999), pp. 829-849.
    by Thomas Hermann, Dinshaw J Patel
    posted to rna structure by ttjoseph on 2006-11-29 22:03:29 as *** along with 3 people and 3 groups marcius condon jarasch beta BioinfoCIPF SGU-CIPF
  • Widespread siRNA "off-target" transcript silencing mediated by seed region sequence complementarity.
    RNA (8 May 2006)
    by Aimee L L Jackson, Julja Burchard, Janell Schelter, B Nelson N Chau, Michele Cleary, Lee Lim, Peter S S Linsley
    posted to rnai by ttjoseph on 2006-11-23 05:07:55 as *** along with 3 people tardigrade lhonigberg mtagaya
  • Structural domains in RNAi.
    FEBS Lett, Vol. 579, No. 26. (31 October 2005), pp. 5841-5849.
    by RE Collins, X Cheng
    posted to rnai by ttjoseph on 2006-11-08 21:22:35 as **
  • Therapeutic RNA interference of malignant melanoma by electrotransfer of small interfering RNA targeting Mitf
    Gene Therapy, Vol. aop, No. current.
    by N Nakai, T Kishida, M Shin-Ya, J Imanishi, Y Ueda, S Kishimoto, O Mazda,
    posted to rnai therapeutics by ttjoseph on 2006-11-01 20:31:08 as **
  • Control of translation and mRNA degradation by miRNAs and siRNAs.
    Genes Dev, Vol. 20, No. 5. (1 March 2006), pp. 515-524.
    by MA Valencia-Sanchez, J Liu, GJ Hannon, R Parker
    posted to argonaute rnai by ttjoseph on 2006-10-30 04:56:49 as *** along with 3 people perrywoo osman bertelsen
  • Argonaute: a scaffold for the function of short regulatory RNAs.
    Trends Biochem Sci (5 October 2006)
    by James S S Parker, David Barford
    posted to argonaute rnai by ttjoseph on 2006-10-29 00:11:33 as ** along with 2 people and 2 groups dchughes mtagaya G4ID Genetics-of-Gambling
  • Argonaute-1 directs siRNA-mediated transcriptional gene silencing in human cells.
    Nat Struct Mol Biol (27 August 2006)
    by Daniel H H Kim, Louisa M M Villeneuve, Kevin V V Morris, John J J Rossi
    posted to argonaute rnai by ttjoseph on 2006-10-29 00:11:13 as ** along with 4 people tardigrade mtagaya elzodw sebastien_vigneau
  • Contributions of 3'-overhang to the dissociation of small interfering RNAs from the PAZ domain: Molecular dynamics simulation study.
    J Mol Graph Model (11 July 2006)
    by Hui Sun S Lee, Soo Nam N Lee, Chul Hyun H Joo, Heuiran Lee, Han Saem S Lee, Seung Yong Y Yoon, Yoo Kyum K Kim, Han Choe
    posted to molecular-dynamics rnai sirna by ttjoseph on 2006-10-12 01:47:11 as *** along with 1 person tardigrade
  • How do substrates enter and products exit the buried active site of cytochrome P450cam? 1. Random expulsion molecular dynamics investigation of ligand access channels and mechanisms
    Journal of Molecular Biology, Vol. 303, No. 5. (10 November 2000), pp. 797-811.
    by Susanna K Ludemann, Valere Lounnas, Rebecca C Wade
    posted to molecular-dynamics remd by ttjoseph on 2006-10-10 23:00:00 as ***
  • From the Cover: Free energy reconstruction from nonequilibrium single-molecule pulling experiments
    PNAS, Vol. 98, No. 7. (27 March 2001), pp. 3658-3661.
    by Gerhard Hummer, Attila Szabo
    posted to biophysics free-energy molecular-dynamics by ttjoseph on 2006-09-29 16:03:20 as *** along with 3 people and 1 group cgguido dchen onufriev WeeksLab
  • Thermodynamic calculations in biological systems
    Biophysical Chemistry, Vol. In Press, Corrected Proof
    by Mario L Amzel, Xavier Siebert, Anthony Armstrong, German Pabon
    posted to biophysics molecular-dynamics by ttjoseph on 2006-09-29 15:59:20 as ** along with 5 people and 3 groups barry pansapiens shuns imouthesmp nknii structural_bioinformatics Bioinformatics TCR_Signaling
  • Structural dynamics of precursor and product of the RNA enzyme from the hepatitis delta virus as revealed by molecular dynamics simulations.
    J Mol Biol, Vol. 351, No. 4. (26 August 2005), pp. 731-748.
    by MV Krasovska, J Sefcikova, N Spacková, J Sponer, NG Walter
    posted to cleavage molecular-dynamics by ttjoseph on 2006-09-29 03:38:01 as ***
  • Kinetics from Nonequilibrium Single-Molecule Pulling Experiments
    Biophys. J., Vol. 85, No. 1. (1 July 2003), pp. 5-15.
    by Gerhard Hummer, Attila Szabo
    posted to biophysics by ttjoseph on 2006-09-29 02:40:39 as ***
  • Calculation of absolute protein-ligand binding free energy from computer simulations.
    Proc Natl Acad Sci U S A, Vol. 102, No. 19. (10 May 2005), pp. 6825-6830.
    by HJ Woo, B Roux
    posted to free-energy molecular-dynamics by ttjoseph on 2006-09-29 00:39:35 as *** along with 3 people LamBras ashaytan ibuch
  • Model-free methods of analyzing domain motions in proteins from simulation: a comparison of normal mode analysis and molecular dynamics simulation of lysozyme.
    Proteins, Vol. 27, No. 3. (March 1997), pp. 425-437.
    by S Hayward, A Kitao, HJ Berendsen
    posted to biophysics collective-dynamics essential-dynamics molecular-dynamics by ttjoseph on 2006-08-18 06:31:09 as ***
  • On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations
    Proteins: Structure, Function, and Genetics, Vol. 36, No. 4. (1999), pp. 419-424.
    by Andrea Amadei, Marc A Ceruso, Alfredo Di Nola
    posted to essential-dynamics molecular-dynamics by ttjoseph on 2006-08-07 18:35:39 as ***
  • Molecular dynamics simulations of biomolecules: long-range electrostatic effects.
    Annu Rev Biophys Biomol Struct, Vol. 28 (1999), pp. 155-179.
    by C Sagui, TA Darden
    posted to electrostatics molecular-dynamics particle-mesh-ewald by ttjoseph on 2006-04-28 21:25:24 as *** along with 6 people onufriev lillekatt dgront RamuAnandakrishnan AndreaColetta r2s2
  • Argonaute and RNA--getting into the groove.
    Curr Opin Struct Biol, Vol. 16, No. 1. (February 2006), pp. 5-11.
    by JJ Song, L Joshua-Tor
    posted to argonaute rnai by ttjoseph on 2006-04-06 01:44:40 as ****
  • Exploring the Helix-Coil Transition via All-Atom Equilibrium Ensemble Simulations.
    Biophys J, Vol. 88, No. 4. (April 2005), pp. 2472-2493.
    by EJ Sorin, VS Pande
    posted to biophysics force-field molecular-dynamics by ttjoseph on 2006-04-03 15:34:45 as ** along with 2 people allmensch loison
  • A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
    Journal of the American Chemical Society, Vol. 117, No. 19. (1995), pp. 5179-5197.
    by Wendy D Cornell, Piotr Cieplak, Christopher I Bayly, Ian R Gould, Kenneth M Merz, David M Ferguson, David C Spellmeyer, Thomas Fox, James W Caldwell, Peter A Kollman
    posted to biophysics force-field by ttjoseph on 2006-04-03 15:33:09 as read
  • Steered molecular dynamics
    Vol. 4 (1998), pp. 39-65.
    by S Izrailev, S Stepaniants, B Isralewitz, D Kosztin, H Lu, F Molnar, W Wriggers, K Schulten
    edited by P Deuflhard, J Hermans, B Leimkuhler, AE Mark, S Reich, RD Skeel
    posted to molecular-dynamics by ttjoseph on 2006-04-01 04:54:39 as ***
  • A heuristic procedure for the detection of locally similar substructures of two equivalent structures.
    Protein Eng, Vol. 7, No. 3. (March 1994), pp. 331-333.
    by M Mezei
    posted to algorithms biophysics flexibility by ttjoseph on 2006-03-31 08:11:19 as read along with 1 person dimka
  • Crystal structure of a PIWI protein suggests mechanisms for siRNA recognition and slicer activity
    The EMBO Journal, Vol. aop, No. current. (02 December 2004)
    by James S Parker, Mark M Roe, David Barford
    posted to argonaute crystal-structure rnai by ttjoseph on 2006-03-31 06:09:13 as ** along with 1 person tardigrade
  • Rapid protein-ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: binding of FK506 to FKBP.
    Proteins, Vol. 54, No. 4. (1 March 2004), pp. 759-767.
    by M Zacharias
    posted to docking essential-dynamics molecular-dynamics by ttjoseph on 2006-03-30 21:15:49 as ** along with 2 people dgruiz RamuAnandakrishnan
  • Comparative study of generalized Born models: protein dynamics.
    Proc Natl Acad Sci U S A, Vol. 102, No. 19. (10 May 2005), pp. 6760-6764.
    by H Fan, AE Mark, J Zhu, B Honig
    posted to generalized-born gromacs by ttjoseph on 2006-03-13 05:22:58 as ***
  • Rigid Protein Motion as a Model for Crystallographic Temperature Factors
    Proceedings of the National Academy of Sciences USA, Vol. 88 (April 1991), pp. 2773-2777.
    by John Kuriyan, William I Weis
    posted to biophysics by ttjoseph on 2006-03-12 16:28:56 as **
  • A note on two problems in connexion with graphs
    Numerische Mathematik, Vol. 1, No. 1. (December 1959), pp. 269-271.
    by EW Dijkstra
    posted to algorithms graph-theory by ttjoseph on 2006-03-09 22:02:04 as ** along with 1 person cari
  • Comparative protein structure modeling of genes and genomes.
    Annu Rev Biophys Biomol Struct, Vol. 29 (2000), pp. 291-325.
    by MA Martí-Renom, AC Stuart, A Fiser, R Sánchez, F Melo, A Sali
    posted to homology-modeling by ttjoseph on 2006-03-09 21:44:40 as ** along with 12 people and 2 groups aalibes nigham chad_davis marcius ffranca duartemolha dgront ruvido insectopalo min013 IrinaMoreira granujilla BioinfoCIPF SGU-CIPF
  • Optimization by Simulated Annealing
    Science, Vol. 220, No. 4598. (1983), pp. 671-680.
    by S Kirkpatrick, Gelatt Cd, Vecchi Mp
    posted to algorithms simulated-annealing by ttjoseph on 2006-02-27 03:01:42 as *** along with 14 people BragilMassoud filippone martinthesis mseise Bc91 ilapla markusd wvangeit andrewmercader fernandohbc slatre guxiyou pawelt dcastro
  • Evidence that siRNAs function as guides, not primers, in the Drosophila and human RNAi pathways.
    Mol Cell, Vol. 10, No. 3. (September 2002), pp. 537-548.
    by DS Schwarz, G Hutvágner, B Haley, PD Zamore
    posted to rnai by ttjoseph on 2006-02-27 00:32:26 as **
  • Structure and conserved RNA binding of the PAZ domain.
    Nature, Vol. 426, No. 6965. (27 November 2003), pp. 468-474.
    by KS Yan, S Yan, A Farooq, A Han, L Zeng, MM Zhou
    posted to rnai by ttjoseph on 2006-02-27 00:23:52 as *** along with 1 person tardigrade
  • Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain
    Nature, Vol. 429, No. 6989. (20 May 2004), pp. 318-322.
    by Jin-Biao Ma, Keqiong Ye, Dinshaw J Patel
    posted to rnai by ttjoseph on 2006-02-26 02:01:04 as ** along with 1 person tardigrade
  • Kinetic analysis of the RNAi enzyme complex.
    Nat Struct Mol Biol, Vol. 11, No. 7. (July 2004), pp. 599-606.
    by B Haley, PD Zamore
    posted to rnai by ttjoseph on 2006-02-26 01:57:19 as ***
  • Specificity of microRNA target selection in translational repression.
    Genes Dev, Vol. 18, No. 5. (1 March 2004), pp. 504-511.
    by JG Doench, PA Sharp
    posted to rnai by ttjoseph on 2006-02-26 01:56:42 as ** along with 3 people evaf tardigrade mtagaya
  • 'Protein Peeling': an approach for splitting a 3D protein structure into compact fragments
    Bioinformatics, Vol. 22, No. 2. (15 January 2006), pp. 129-133.
    by Jean-Christophe Gelly, Alexandre G de Brevern, Serge Hazout
    posted to algorithms by ttjoseph on 2006-02-01 23:01:26 as *** along with 7 people and 4 groups MarcoAlvarez ana barry dimka marcius nickolay choonpeng structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
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