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LamBras md [51 articles]

Recent papers added to LamBras library classified by the tag md. You can also see everyone's md.
  • Molecular Dynamics Simulations of Proteins: Can the Explicit Water Model Be Varied?
    J. Chem. Theory Comput., Vol. 3, No. 4. (10 July 2007), pp. 1550-1560.
    by DR Nutt, JC Smith
    posted to md by LamBras on 2008-08-11 21:06:20 as ***** along with 2 people onufriev softsimu
  • Advances in biomolecular simulations: methodology and recent applications.
    Q Rev Biophys, Vol. 36, No. 3. (August 2003), pp. 257-306.
    by J Norberg, L Nilsson
    posted to review md by LamBras on 2008-08-11 20:53:21 as ***** along with 2 people baaden ltrabuco
  • Biomolecular modeling: Goals, problems, perspectives.
    Angew Chem Int Ed Engl, Vol. 45, No. 25. (19 June 2006), pp. 4064-4092.
    by WF van Gunsteren, D Bakowies, R Baron, I Chandrasekhar, M Christen, X Daura, P Gee, DP Geerke, A Glättli, PH Hünenberger, MA Kastenholz, C Oostenbrink, M Schenk, D Trzesniak, NF van der Vegt, HB Yu
    posted to review md by LamBras on 2008-08-11 20:51:57 as ***** along with 1 person patricia
  • Molecular dynamics: survey of methods for simulating the activity of proteins.
    Chem Rev, Vol. 106, No. 5. (May 2006), pp. 1589-1615.
    by SA Adcock, JA McCammon
    posted to review md by LamBras on 2008-08-11 20:50:31 as ***** along with 2 people higueruelo aqeel
  • 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 normal_modes md by LamBras on 2008-07-24 12:31:31 as *** along with 1 person higueruelo
  • Molecular dynamics simulations of ethanol binding to the transmembrane domain of the glycine receptor: Implications for the channel potentiation mechanism
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Mary H Cheng, Rob D Coalson, Michael Cascio
    posted to md by LamBras on 2008-07-20 16:15:14 as ** along with 1 person RamuAnandakrishnan
  • Microsecond-to-Millisecond Conformational Dynamics Demarcate the GluR2 Glutamate Receptor Bound to Agonists Glutamate, Quisqualate, and AMPA
    Biochemistry, Vol. 44, No. 9. (8 March 2005), pp. 3410-3417.
    by ER Valentine, AG Palmer
    posted to md ion_channels dynamics by LamBras on 2008-07-20 15:33:56 as ** along with 1 person rph
  • A dynamic model for the allosteric mechanism of GroEL.
    J Mol Biol, Vol. 302, No. 2. (15 September 2000), pp. 303-313.
    by J Ma, PB Sigler, Z Xu, M Karplus
    posted to targeted_md md by LamBras on 2008-07-20 15:11:27 as **** along with 2 people lna dgront
  • Molecular Dynamics Simulations of the Ligand-Binding Domain of the Ionotropic Glutamate Receptor GluR2
    Biophys. J., Vol. 82, No. 2. (1 February 2002), pp. 676-683.
    by Yalini Arinaminpathy, Mark S Sansom, Philip C Biggin
    posted to nmda md by LamBras on 2008-07-20 15:06:57 as **
  • Molecular dynamics simulations of biomolecules.
    Nat Struct Biol, Vol. 9, No. 9. (September 2002), pp. 646-652.
    by M Karplus, JA McCammon
    posted to review md by LamBras on 2008-07-17 18:05:33 as ***** along with 4 people RamuAnandakrishnan baaden aqeel simone
  • Targeted molecular dynamics simulation studies of binding and conformational changes in <I>E. coli</I> MurD
    Proteins: Structure, Function, and Bioinformatics, Vol. 68, No. 1. (2007), pp. 243-254.
    by Andrej Perdih, Miha Kotnik, Milan Hodoscek, Tom Solmajer
    posted to targeted_md md by LamBras on 2008-07-17 18:00:23 as **
  • Extending the capabilities of targeted molecular dynamics: Simulation of a large conformational transition in plasminogen activator inhibitor 1
    Protein Sci, Vol. 10, No. 4. (1 April 2001), pp. 798-808.
    by Peter Kruger, Stefan Verheyden, Paul J Declerck, Yves Engelborghs
    posted to targeted_md md by LamBras on 2008-07-17 17:58:24 as ** along with 1 person ruvido
  • Targeted Molecular Dynamics Simulation of Conformational Change-Application to the T ↔ R Transition in Insulin
    Molecular Simulation, Vol. 10, No. 2. (1993), pp. 291-308.
    by J Schlitter, M Engels, P Krüger, E Jacoby, A Wollmer
    posted to targeted_md md by LamBras on 2008-07-17 17:56:50 as **
  • Steered molecular dynamics investigations of protein function
    Journal of Molecular Graphics and Modelling, Vol. 19, No. 1. (February 2001), pp. 13-25.
    by Barry Isralewitz, Jerome Baudry, Justin Gullingsrud, Dorina Kosztin, Klaus Schulten
    posted to targeted_md md by LamBras on 2008-07-17 17:55:50 as ** along with 1 person choonpeng
  • 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 targeted_md md by LamBras on 2008-07-17 17:54:26 as ** along with 2 people and 2 groups barry ttjoseph structural_bioinformatics Bioinformatics
  • Targeted molecular dynamics: A new approach for searching pathways of conformational transitions
    Journal of Molecular Graphics, Vol. 12, No. 2. (June 1994), pp. 84-89.
    by J Schlitter, M Engels, P Kruger
    posted to targeted_md md by LamBras on 2008-07-17 17:53:07 as ** along with 1 person cactus
  • Computer simulations of protein folding by targeted molecular dynamics
    Proteins: Structure, Function, and Genetics, Vol. 39, No. 3. (2000), pp. 252-260.
    by Philippe Ferrara, Joannis Apostolakis, Amedeo Caflisch
    posted to targeted_md md by LamBras on 2008-07-17 17:51:25 as **
  • Role of the Active-Site Solvent in the Thermodynamics of Factor Xa Ligand Binding
    J. Am. Chem. Soc., Vol. 130, No. 9. (5 March 2008), pp. 2817-2831.
    by R Abel, T Young, R Farid, BJ Berne, RA Friesner
    posted to md free_energy by LamBras on 2008-07-15 15:47:18 as ****
  • An improved relaxed complex scheme for receptor flexibility in computer-aided drug design.
    J Comput Aided Mol Des (15 January 2008)
    by Rommie E Amaro, Riccardo Baron, J A McCammon
    posted to md flexibility docking by LamBras on 2008-07-04 11:00:17 as ** along with 2 people higueruelo kazemi
  • Molecular dynamics simulations of LysRS: An asymmetric state
    Proteins: Structure, Function, and Bioinformatics, Vol. 62, No. 3. (29 November 2005), 662.
    by SJ Hughes, JA Tanner, AD Miller, IR Gould
    posted to trna md by LamBras on 2008-06-10 16:06:08 as **
  • Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation
    Current Opinion in Structural Biology, Vol. 17, No. 6. (December 2007), pp. 633-640.
    by Ivet Bahar, Chakra Chennubhotla, Dror Tobi
    posted to md flexibility allosteric by LamBras on 2008-04-25 14:35:05 as *** along with 7 people and 3 groups higueruelo barry aqeel ruvido cactus sobolevnrm jennifermbui structural_bioinformatics Bioinformatics baker-group
  • 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 md by LamBras on 2008-04-25 14:33:01 as ** along with 12 people and 2 groups lna dimka aqeel aswin rabio grahamc hmk zwang biehl Ema phoenixzxl ras ParkinsonLab_at_MaRS The BMM Dome
  • Can molecular dynamics simulations help in discriminating correct from erroneous protein 3D models?
    BMC Bioinformatics, Vol. 9 (07 January 2008), 6.
    by Jean-Francois Taly, Antoine Marin, Jean-Francois Gibrat
    posted to md by LamBras on 2008-04-25 14:32:39 as ** along with 1 person biehl
  • Molecular dynamics simulations of ligand-induced backbone conformational changes in the binding site of the periplasmic lysine-, arginine-, ornithine-binding protein
    Journal of Computer-Aided Molecular Design
    by Ami Yang, Ricardo Mancera
    posted to md flexibility by LamBras on 2008-04-24 15:31:32 as **
  • Mechanism of Na+/H+ Antiporting
    Science, Vol. 317, No. 5839. (10 August 2007), pp. 799-803.
    by Isaiah T Arkin, Huafeng Xu, Morten O Jensen, Eyal Arbely, Estelle R Bennett, Kevin J Bowers, Edmond Chow, Ron O Dror, Michael P Eastwood, Ravenna Flitman-Tene, Brent A Gregersen, John L Klepeis, Istvan Kolossvary, Yibing Shan, David E Shaw
    posted to md by LamBras on 2008-04-03 09:22:43 as ** along with 4 people and 1 group dimka sobolevnrm Jporci MMehrotra baker-group
  • Microsecond Molecular Dynamics Simulation Shows Effect of Slow Loop Dynamics on Backbone Amide Order Parameters of Proteins
    J. Phys. Chem. B (1 March 2008)
    by P Maragakis, K Lindorff-Larsen, MP Eastwood, RO Dror, JL Klepeis, IT Arkin, MO Jensen, H Xu, N Trbovic, RA Friesner, AG Palmer, DE Shaw
    posted to md by LamBras on 2008-04-03 09:22:08 as ** along with 1 person and 1 group skoddet Nielsen group
  • Force Field Validation Using Protein Side Chain Prediction
    J. Phys. Chem. B, Vol. 106, No. 44. (7 November 2002), pp. 11673-11680.
    by MP Jacobson, GA Kaminski, RA Friesner, CS Rapp
    posted to forcefield md sidechain by LamBras on 2008-03-22 16:09:35 as ****
  • Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides
    J. Phys. Chem. B, Vol. 105, No. 28. (19 July 2001), pp. 6474-6487.
    by GA Kaminski, RA Friesner, J Tirado-Rives, WL Jorgensen
    posted to forcefield md by LamBras on 2008-03-22 16:06:30 as *****
  • Structural analysis of protein dynamics by MD simulations and NMR spin-relaxation
    Proteins: Structure, Function, and Bioinformatics, Vol. 71, No. 2. (1 November 2007), pp. 684-694.
    by Nikola Trbovic, Byungchan Kim, Richard A Friesner, Arthur G Palmer
    posted to md nmr by LamBras on 2008-03-20 19:53:17 as **
  • Probing ligand binding modes of human cytochrome P450 2J2 by homology modeling, molecular dynamics simulation, and flexible molecular docking
    Proteins: Structure, Function, and Bioinformatics, Vol. 71, No. 2. (14 November 2007), pp. 938-949.
    by Weihua Li, Yun Tang, Hong Liu, Jiagao Cheng, Weiliang Zhu, Hualiang Jiang
    posted to docking homology_modeling md by LamBras on 2008-03-20 19:37:17 as ***
  • Protein flexibility and dynamics using constraint theory
    J Mol Graph Model, Vol. 19, No. 1. (2001), pp. 60-69.
    by MF Thorpe, M Lei, AJ Rader, DJ Jacobs, LA Kuhn
    posted to md flexibility by LamBras on 2008-03-15 16:27:11 as **
  • A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor
    J Comput Chem, Vol. 25, No. 16. (2004), pp. 1995-2005.
    by R Tatsumi, Y Fukunishi, H Nakamura
    posted to md hd flexibility by LamBras on 2008-03-15 16:27:11 as **
  • Probing flexibility and ?induced-fit? phenomena in aldose reductase by comparative crystal structure analysis and molecular dynamics simulations
    Proteins: Structure, Function, and Bioinformatics, Vol. 56, No. 1. (2004), pp. 52-66.
    by Christoph Sotriffer, Oliver Krã¤mer, Gerhard Klebe
    posted to md flexibility docking by LamBras on 2008-03-15 16:27:11 as **
  • Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms
    J. Chem. Theory Comput. (2007)
    by J Shao, SW Tanner, N Thompson, TE Cheatham
    posted to md clustering by LamBras on 2008-03-15 16:27:11 as **
  • Wordom: a program for efficient analysis of molecular dynamics simulations
    Bioinformatics, Vol. 23, No. 19. (2007), pp. 2625-2627.
    by Michele Seeber, Marco Cecchini, Francesco Rao, Giovanni Settanni, Amedeo Caflisch
    posted to md by LamBras on 2008-03-15 16:27:11 as **
  • Calculation of ligand binding free energies from molecular dynamics simulations
    International Journal of Quantum Chemistry, Vol. 69, No. 1. (1998), pp. 77-88.
    by J Marelius, T Hansson, J Ã…qvist
    posted to md free_energy by LamBras on 2008-03-15 16:27:10 as **
  • Protein flexibility using constraints from molecular dynamics simulations
    Phys Biol, Vol. 2, No. 4. (2005)
    by T Mamonova, B Hespenheide, R Straub, MF Thorpe, M Kurnikova
    posted to md flexibility by LamBras on 2008-03-15 16:27:10 as **
  • Full correlation analysis of conformational protein dynamics
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007)
    by Oliver Lange, Helmut Grubmã¼ller
    posted to normal_modes md by LamBras on 2008-03-15 16:27:10 as **
  • Protein flexibility: its role in structure and mechanism revealed by molecular simulations
    Cell Mol Life Sci, Vol. 63, No. 2. (2006), pp. 207-219.
    by G Dodson, CS Verma
    posted to md flexibility by LamBras on 2008-03-15 16:27:08 as *****
  • Combining docking and molecular dynamic simulations in drug design
    Med Res Rev (2006)
    by Hernã¡n Alonso, Andrey A Bliznyuk, Jill E Gready
    posted to md docking by LamBras on 2008-03-15 16:27:08 as *****
  • Molecular dynamics simulations of the ligand-binding domain of an N-methyl-D-aspartate receptor.
    J Biol Chem, Vol. 281, No. 18. (5 May 2006), pp. 12736-12742.
    by SL Kaye, MS Sansom, PC Biggin
    posted to md nmda by LamBras on 2008-03-07 10:54:56 as *****
  • Full correlation analysis of conformational protein dynamics
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Oliver F Lange, Helmut Grubmüller
    posted to md normal_modes by LamBras on 2008-02-24 17:34:10 as ** along with 3 people and 1 group barry choonpeng sobolevnrm baker-group
  • Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms
    J. Chem. Theory Comput. (6 October 2007)
    by J Shao, SW Tanner, N Thompson, TE Cheatham
    posted to clustering md by LamBras on 2008-02-24 17:33:47 as ** along with 5 people and 2 groups GermanErlenkamp allmensch barry daevans sobolevnrm structural_bioinformatics baker-group
  • 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 md by LamBras on 2008-02-24 17:33:30 as ** along with 6 people and 2 groups jyuh barry tmmurali choonpeng hmk sobolevnrm structural_bioinformatics baker-group
  • Probing flexibility and ?induced-fit? phenomena in aldose reductase by comparative crystal structure analysis and molecular dynamics simulations
    Proteins: Structure, Function, and Bioinformatics, Vol. 56, No. 1. (2004), pp. 52-66.
    by Christoph A Sotriffer, Oliver Krämer, Gerhard Klebe
    posted to docking flexibility md by LamBras on 2008-01-24 15:12:31 as **** along with 2 people aqeel kazemi
  • Calculation of ligand binding free energies from molecular dynamics simulations
    International Journal of Quantum Chemistry, Vol. 69, No. 1. (1998), pp. 77-88.
    by J Marelius, T Hansson, J Åqvist
    posted to free_energy md by LamBras on 2007-11-23 12:41:12 as ** along with 1 person kazemi
  • A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor.
    J Comput Chem, Vol. 25, No. 16. (December 2004), pp. 1995-2005.
    by R Tatsumi, Y Fukunishi, H Nakamura
    posted to flexibility hd md by LamBras on 2007-11-23 12:40:52 as ** along with 2 people aqeel kazemi
  • Combining docking and molecular dynamic simulations in drug design.
    Med Res Rev (6 June 2006)
    by Hernán Alonso, Andrey A A Bliznyuk, Jill E E Gready
    posted to docking md by LamBras on 2007-11-23 12:39:01 as ***** along with 3 people and 1 group aqeel yongzhao kazemi TSRI_MGL
  • Protein flexibility: its role in structure and mechanism revealed by molecular simulations.
    Cell Mol Life Sci, Vol. 63, No. 2. (January 2006), pp. 207-219.
    by G Dodson, CS Verma
    posted to flexibility md by LamBras on 2007-11-20 12:44:21 as ** along with 1 person allmensch
  • Protein flexibility and dynamics using constraint theory.
    J Mol Graph Model, Vol. 19, No. 1. (2001), pp. 60-69.
    by MF Thorpe, M Lei, AJ Rader, DJ Jacobs, LA Kuhn
    posted to flexibility md by LamBras on 2007-11-20 12:44:09 as ** along with 4 people higueruelo lna aqeel blackbart
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