bmduggan's molecular-dynamics [60 articles] Export Sort

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	Targeted molecular dynamics: a new approach for searching pathways of conformational transitions. [My Copy] Journal of molecular graphics, Vol. 12, No. 2. (June 1994), pp. 84-89. by J. Schlitter, M. Engels, P. Krüger posted to targeted molecular-dynamics by bmduggan on 2009-11-07 03:54:58 as
	Computational design of affinity and specificity at protein–protein interfaces [My Copy] Current Opinion in Structural Biology, Vol. 19, No. 4. (29 August 2009), pp. 458-463. by John Karanicolas, Brian Kuhlman posted to rosetta review molecular-dynamics interactions design by bmduggan on 2009-10-28 15:28:08 as along with 4 people sobolevnrm VGreiff higueruelo barry
	Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations [My Copy] Proceedings of the National Academy of Sciences, Vol. 103, No. 32. (8 August 2006), pp. 11844-11849. by Kei-ichi Okazaki, Nobuyasu Koga, Shoji Takada, Jose N. Onuchic, Peter G. Wolynes posted to molecular-dynamics by bmduggan on 2009-09-23 21:22:27 as along with 3 people and 1 group allmensch choonpeng joseph_x_zhou protein_Dyn
	Mechanism of Acetylcholinesterase Inhibition by Fasciculin: A 5-ns Molecular Dynamics Simulation [My Copy] Journal of the American Chemical Society, Vol. 124, No. 21. (1 May 2002), pp. 6153-6161. by Kaihsu Tai, Tongye Shen, Richard H. Henchman, Yves Bourne, Pascale Marchot, J. Andrew McCammon posted to molecular-dynamics allostery by bmduggan on 2009-09-15 20:59:29 as along with 1 person ffranca
	Validation of Molecular Dynamics Simulations of Biomolecules Using NMR Spin Relaxation as Benchmarks: Application to the AMBER99SB Force Field [My Copy] Journal of Chemical Theory and Computation, Vol. 3, No. 3. (1 May 2007), pp. 961-975. by Scott A. Showalter, Rafael Bruschweiler posted to relaxation nmr molecular-dynamics ff99sb by bmduggan on 2009-09-10 02:12:22 as along with 3 people allmensch pablocarb loison
	Bornyl (3,4,5-trihydroxy)-cinnamate--an optimized human neutrophil elastase inhibitor designed by free energy calculations. [My Copy] Bioorganic & medicinal chemistry, Vol. 16, No. 5. (1 March 2008), pp. 2385-2390. by Thomas Steinbrecher, Andrea Hrenn, Korinna L. Dormann, Irmgard Merfort, Andreas Labahn posted to thermodynamic-integration molecular-dynamics interactions docking by bmduggan on 2009-09-08 20:24:03 as along with 1 person dmobley
	A multistep approach to structure-based drug design: studying ligand binding at the human neutrophil elastase. [My Copy] Journal of medicinal chemistry, Vol. 49, No. 6. (23 March 2006), pp. 1837-1844. by Thomas Steinbrecher, David A. Case, Andreas Labahn posted to thermodynamic-integration molecular-dynamics mmpbsa docking by bmduggan on 2009-09-08 20:23:12 as along with 1 person bilab
	Anatomy of a structural pathway for activation of the catalytic domain of Src kinase Hck [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 67, No. 4. (1 June 2007), pp. 1096-1112. by Nilesh K. Banavali, Benoît Roux posted to targeted sampling molecular-dynamics interactions allostery by bmduggan on 2009-09-04 15:33:12 as along with 3 people allmensch choonpeng ruvido
	Fast peptidyl cis-trans isomerization within the flexible Gly-rich flaps of HIV-1 protease. [My Copy] Journal of the American Chemical Society, Vol. 127, No. 40. (12 October 2005), pp. 13778-13779. by Donald Hamelberg, J. Andrew Mccammon posted to molecular-dynamics accelerated by bmduggan on 2009-09-03 20:26:29 as along with 1 person pgasper
	Estimating kinetic rates from accelerated molecular dynamics simulations: Alanine dipeptide in explicit solvent as a case study [My Copy] The Journal of Chemical Physics, Vol. 127, No. 17. (2007), 175105. by César Augusto, Donald Hamelberg, J. Andrew Mccammon posted to sampling molecular-dynamics accelerated by bmduggan on 2009-09-03 20:06:57 as along with 1 person and 1 group sobolevnrm baker-group
	Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 106, No. 10. (10 March 2009), pp. 3776-3781. by Sichun Yang, Nilesh K. Banavali, Benoît Roux posted to sampling multicopy molecular-dynamics by bmduggan on 2009-09-03 19:55:16 as along with 7 people and 2 groups anuragsethi Diego_Prada allmensch guhjy sobolevnrm barry jmccammon baker-group McCammon
	Locally accessible conformations of proteins: multiple molecular dynamics simulations of crambin. [My Copy] Protein Science, Vol. 7, No. 3. (March 1998), pp. 649-666. by L. S. Caves, J. D. Evanseck, M. Karplus posted to sampling multicopy molecular-dynamics by bmduggan on 2009-09-03 19:43:33 as along with 4 people sunnytov lillekatt allmensch toerst
	Elucidating the inhibition mechanism of HIV-1 non-nucleoside reverse transcriptase inhibitors through multicopy molecular dynamics simulations. [My Copy] Journal of molecular biology, Vol. 388, No. 3. (8 May 2009), pp. 644-658. by Anthony Ivetac, J. Andrew McCammon posted to sampling multicopy molecular-dynamics by bmduggan on 2009-09-03 19:36:44 as along with 4 people and 1 group ahmetbakan nfparrish sobolevnrm paulschlesinger baker-group
	Long-timescale molecular dynamics simulations of protein structure and function. [My Copy] Current opinion in structural biology, Vol. 19, No. 2. (08 April 2009), pp. 120-127. by John L. Klepeis, Kresten Lindorff-Larsen, Ron O. Dror, David E. Shaw posted to sampling molecular-dynamics convergence by bmduggan on 2009-09-03 19:15:38 as along with 12 people and 1 group loison xdeupi agrossfield allmensch r2s2 apaydin kiekyon Borelli idoerg sobolevnrm edws paulschlesinger baker-group
	Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects: calculation of structural and dynamic properties. [My Copy] Proteins, Vol. 60, No. 3. (15 August 2005), pp. 464-484. by Xianfeng Li, Sergio A. Hassan, Ernest L. Mehler posted to sampling molecular-dynamics convergence by bmduggan on 2009-09-03 17:16:33 as along with 3 people jjurban flbarroso baaden
	Assessing equilibration and convergence in biomolecular simulations. [My Copy] Proteins, Vol. 48, No. 3. (15 August 2002), pp. 487-496. by Lorna J. Smith, Xavier Daura, Wilfred F. van Gunsteren posted to sampling multicopy molecular-dynamics convergence by bmduggan on 2009-09-03 17:13:38 as along with 3 people and 2 groups sobolevnrm oteri mleis baker-group Structural Biology Group TorVergata
	Molecular simulation of multistate peptide dynamics: A comparison between microsecond timescale sampling and multiple shorter trajectories [My Copy] Journal of Computational Chemistry, Vol. 29, No. 11. (August 2008), pp. 1740-1752. by Luca Monticelli, Eric J. Sorin, D. Peter Tieleman, Vijay S. Pande, Giorgio Colombo posted to sampling multicopy molecular-dynamics by bmduggan on 2009-09-03 17:11:44 as along with 2 people and 1 group arnaucordomi sobolevnrm baker-group
	High-resolution structure prediction and the crystallographic phase problem [My Copy] Nature, Vol. 450, No. 7167. (14 October 2007), pp. 259-264. by Bin Qian, Srivatsan Raman, Rhiju Das, et al.Philip Bradley, Airlie J. McCoy, Randy J. Read, David Baker posted to structure-prediction rosetta molecular-dynamics by bmduggan on 2009-09-02 19:58:03 as along with 16 people and 2 groups newton1234 apaydin aheilbut jwm eckart_bindewald ffranca dgront massivemayhem cjeans zwang cactus sobolevnrm boris_aguilar Ema chenway ardalby baker-group OPIG
	Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 32. (12 August 2008), pp. 11182-11187. by Kei-ichi Okazaki, Shoji Takada posted to molecular-dynamics allostery by bmduggan on 2009-09-01 20:52:53 as along with 9 people and 2 groups mittinatten oteri xdeupi okapi aqeel raik ruvido barry zwang structural_bioinformatics McCammon
	Conformational transition pathway in the allosteric process of calcium-induced recoverin: Molecular dynamics simulations [My Copy] Journal of Computational Chemistry, Vol. 30, No. 7. (2009), pp. 1135-1145. by Ji-Lai Li, Cai-Yun Geng, Yuxiang Bu, Xu-Ri Huang, Chia-Chung Sun posted to molecular-dynamics allostery by bmduggan on 2009-09-01 20:40:43 as
	Particle mesh Ewald: An N-log(N) method for Ewald sums in large systems [My Copy] The Journal of Chemical Physics, Vol. 98, No. 12. (1993), pp. 10089-10092. by Tom Darden, Darrin York, Lee Pedersen posted to molecular-dynamics by bmduggan on 2009-08-31 21:51:02 as along with 13 people anallam sunnytov rpetrenko r2s2 robertvacha A_Coletta_Thesis mleis and_ped10 allmensch easybakemuffin RamuAnandakrishnan tji ashaytan
	Comparison of simple potential functions for simulating liquid water [My Copy] 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 tip3p molecular-dynamics by bmduggan on 2009-08-31 21:24:57 as along with 17 people and 1 group jmparks fralium kulinskii ibuch Lombardo_7 paddydu dfgreen softsimu mleis ttjoseph ffranca easybakemuffin ashaytan RamuAnandakrishnan r2s2 pavanghatty Diego_Prada CMB
	Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew [My Copy] The Journal of Chemical Physics, Vol. 120, No. 20. (2004), pp. 9665-9678. by Hans W. Horn, William C. Swope, Jed W. Pitera, et al.Jeffry D. Madura, Thomas J. Dick, Greg L. Hura, Teresa H. Gordon posted to tip4p molecular-dynamics by bmduggan on 2009-08-31 17:23:42 as along with 3 people and 1 group Lombardo_7 whitead softsimu Jiang Research Group
	Amber 10 [My Copy] by David A. Case, T. A. Darden, T. E. Cheatham, et al.Carlos L. Simmerling, J. Wang, Robert E. Duke, Ray Luo, Michael Crowley, Ross C. Walker, W. Zhang, K. M. Merz, B. Wang, S. Hayik, Adrian Roitberg, Gustavo Seabra, I. Kolossváry, K. F. Wong, F. Paesani, J. Vanicek, X. Wu, Scott R. Brozell, Tom Steinbrecher, Holger Gohlke, L. Yang, C. Tan, J. Mongan, V. Hornak, G. Cui, D. H. Mathews, M. G. Seetin, C. Sagui, V. Babin, Peter A. Kollman posted to molecular-dynamics by bmduggan on 2009-08-31 17:13:32 as
	Exploring Multiple Timescale Motions in Protein GB3 Using Accelerated Molecular Dynamics and NMR Spectroscopy [My Copy] Journal of the American Chemical Society, Vol. 129, No. 15. (1 April 2007), pp. 4724-4730. by Phineus R. L. Markwick, Guillaume Bouvignies, Martin Blackledge posted to nmr molecular-dynamics accelerated by bmduggan on 2009-08-24 19:31:53 as along with 2 people rph RamuAnandakrishnan
	Molecular simulations of protein dynamics: new windows on mechanisms in biology. [My Copy] EMBO reports, Vol. 9, No. 2. (February 2008), pp. 144-150. by G. G. Dodson, D. P. Lane, C. S. Verma posted to review molecular-dynamics by bmduggan on 2009-07-28 19:08:33 as
	Protein Side-Chain Dynamics and Residual Conformational Entropy [My Copy] Journal of the American Chemical Society, Vol. 131, No. 2. (21 January 2009), pp. 615-622. by Nikola Trbovic, Jae-Hyun Cho, Robert Abel, Richard A. Friesner, Mark Rance, Arthur G. Palmer posted to molecular-dynamics nmr by bmduggan on 2009-07-27 15:26:07 as along with 2 people and 3 groups barry sobolevnrm structural_bioinformatics McCammon baker-group
	Evaluating Rotational Diffusion from Protein MD Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 112, No. 19. (1 May 2008), pp. 6013-6024. by Vance Wong, David A. Case posted to tip4p molecular-dynamics by bmduggan on 2009-07-27 15:20:19 as along with 1 person pavanghatty
	Impact of Cl- and Na+ ions on simulated structure and dynamics of βARK1 PH domain [My Copy] Proteins: Structure, Function, and Genetics, Vol. 35, No. 2. (1999), pp. 206-217. by Stefania Pfeiffer, David Fushman, David Cowburn posted to molecular-dynamics by bmduggan on 2009-07-21 20:54:00 as
	Simulated and NMR-Derived Backbone Dynamics of a Protein with Significant Flexibility: A Comparison of Spectral Densities for the βARK1 PH Domain [My Copy] Journal of the American Chemical Society, Vol. 123, No. 13. (1 April 2001), pp. 3021-3036. by Stefania Pfeiffer, David Fushman, David Cowburn posted to molecular-dynamics nmr relaxation by bmduggan on 2009-07-21 20:52:42 as
	Effects of ligand binding on the dynamics of rice nonspecific lipid transfer protein 1: A model from molecular simulations [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 72, No. 4. (2008), pp. 1189-1198. by Yen-Ting Lai, Chao-Sheng Cheng, Yu-Nan Liu, Yaw-Jen Liu, Ping-Chiang Lyu posted to molecular-dynamics by bmduggan on 2009-07-10 03:14:52 as
	Analysis of the Structural and Dynamic Properties of Human N-Terminal Domain of Apolipoprotein E by Molecular Dynamics Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 112, No. 29. (1 July 2008), pp. 8730-8736. by Isabelle Ortmans, Martine Prévost posted to molecular-dynamics by bmduggan on 2009-07-10 03:08:03 as
	Investigating protein dynamics in collective coordinate space [My Copy] Current Opinion in Structural Biology, Vol. 9, No. 2. (April 1999), pp. 164-169. by A. Kitao, N. Go posted to molecular-dynamics by bmduggan on 2009-07-10 02:58:39 as along with 6 people and 1 group Scis0000002 ttjoseph ffranca barry choonpeng sobolevnrm baker-group
	Collective protein dynamics in relation to function [My Copy] Current Opinion in Structural Biology, Vol. 10, No. 2. (1 April 2000), pp. 165-169. by Herman J. C. Berendsen, Steven Hayward posted to molecular-dynamics by bmduggan on 2009-07-10 02:14:28 as along with 2 people aqeel barry
	Are there non-trivial dynamic cross-correlations in proteins? [My Copy] Journal of Molecular Biology, Vol. 279, No. 4. (19 June 1998), pp. 911-920. by Roger Abseher, Michael Nilges posted to molecular-dynamics by bmduggan on 2009-07-10 02:13:57 as
	Fluctuation and Cross-correlation Analysis of Protein Motions Observed in Nanosecond Molecular Dynamics Simulations [My Copy] Journal of Molecular Biology, Vol. 252, No. 4. (29 September 1995), pp. 492-503. by P. Hünenberger posted to molecular-dynamics by bmduggan on 2009-07-07 04:28:06 as along with 1 person aqeel
	Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. [My Copy] Journal of Molecular Biology, Vol. 330, No. 4. (18 July 2003), pp. 891-913. by H. Gohlke, C. Kiel, D. A. Case posted to interactions mmpbsa molecular-dynamics by bmduggan on 2009-06-03 22:07:57 as along with 2 people onufriev lillekatt
	Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf. [My Copy] Journal of computational chemistry, Vol. 25, No. 2. (30 January 2004), pp. 238-250. by H. Gohlke, D. A. Case posted to interactions mmpbsa molecular-dynamics by bmduggan on 2009-06-03 22:07:30 as along with 3 people flbarroso onufriev lillekatt
	Change in protein flexibility upon complex formation: analysis of Ras-Raf using molecular dynamics and a molecular framework approach. [My Copy] Proteins, Vol. 56, No. 2. (1 August 2004), pp. 322-337. by H. Gohlke, L. A. Kuhn, D. A. Case posted to interactions molecular-dynamics by bmduggan on 2009-06-03 22:05:28 as along with 4 people and 2 groups barry lna aqeel blackbart structural_bioinformatics Bioinformatics
	Three-dimensional structure of a glycosphingolipid having a novel carbohydrate linkage, Galbeta1-4(Fucalpha1-3)Glcbeta1-3Galbeta, determined by theoretical calculations. [My Copy] Glycoconjugate journal, Vol. 15, No. 2. (February 1998), pp. 107-113. by J. Kawakami, Y. Kawakami, K. Nakamura, H. Kojima, S. Ito, Y. Tamai posted to molecular-dynamics nmr sphingolipid by bmduggan on 2009-03-26 13:32:44 as
	Protein Dynamics in Enzymatic Catalysis: Exploration of Dihydrofolate Reductase [My Copy] Journal of the American Chemical Society, Vol. 122, No. 2. (1 January 2000), pp. 225-231. by Jennifer L. Radkiewicz, Charles L. Brooks posted to dhfr molecular-dynamics by bmduggan on 2009-03-05 04:02:42 as along with 1 person paulymer
	Structure and dynamics of zymogen human blood coagulation factor X. [My Copy] Biophysical Journal, Vol. 82, No. 3. (March 2002), pp. 1190-1206. by D. Venkateswarlu, L. Perera, T. Darden, L. G. Pedersen posted to factorx molecular-dynamics by bmduggan on 2009-02-01 02:39:04 as
	A combined structural dynamics approach identifies a putative switch in factor VIIa employed by tissue factor to initiate blood coagulation. [My Copy] Protein Science, Vol. 16, No. 4. (April 2007), pp. 671-682. by O. H. Olsen, K. D. Rand, H. Østergaard, E. Persson posted to factorvii molecular-dynamics tissuefactor by bmduggan on 2009-01-28 14:44:44 as
	Comparison of multiple Amber force fields and development of improved protein backbone parameters. [My Copy] Proteins, Vol. 65, No. 3. (15 November 2006), pp. 712-725. by Viktor Hornak, Robert Abel, Asim Okur, Bentley Strockbine, Adrian Roitberg, Carlos Simmerling posted to molecular-dynamics ff99sb by bmduggan on 2009-01-22 16:44:14 as along with 10 people arnaucordomi Vadikus baaden lna allmensch choonpeng kazemi barry GermanErlenkamp RamuAnandakrishnan
	Structure and thermodynamics of RNA-protein binding: using molecular dynamics and free energy analyses to calculate the free energies of binding and conformational change. [My Copy] Journal of Molecular Biology, Vol. 297, No. 5. (14 April 2000), pp. 1145-1158. by C. M. Reyes, P. A. Kollman posted to mmpbsa molecular-dynamics by bmduggan on 2009-01-09 19:49:31 as along with 2 people balewis dfgreen
	Refinement of NMR structures using implicit solvent and advanced sampling techniques. [My Copy] Journal of the American Chemical Society, Vol. 126, No. 49. (15 December 2004), pp. 16038-16047. by J. Chen, W. Im, C. L. Brooks posted to molecular-dynamics nmr by bmduggan on 2009-01-09 19:41:18 as along with 2 people baaden bilab
	Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes [My Copy] Journal of Computational Physics, Vol. 23, No. 3. (March 1977), pp. 327-341. by J. Ryckaert, G. Ciccotti, H. Berendsen posted to shake molecular-dynamics by bmduggan on 2008-12-29 18:33:44 as along with 8 people Vadikus dimka rpetrenko choonpeng gcottone stephenbond A_Coletta_Thesis ashaytan
	Structural biology by NMR: structure, dynamics, and interactions. [My Copy] PLoS Computational Biology, Vol. 4, No. 9. (September 2008) by P. R. Markwick, T. Malliavin, M. Nilges posted to molecular-dynamics nmr relaxation by bmduggan on 2008-11-29 01:41:42 as along with 8 people and 1 group rph betainverse pengchy raik ruvido zwang laurabailey barry structural_bioinformatics
	Accuracy and precision of NMR relaxation experiments and MD simulations for characterizing protein dynamics [My Copy] Proteins: Structure, Function, and Genetics, Vol. 28, No. 4. (1997), pp. 481-493. by Marios Philippopoulos, Arthur M. Mandel, Arthur G. Palmer, Carmay Lim posted to molecular-dynamics nmr relaxation by bmduggan on 2008-11-29 00:59:12 as
	Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate-DNA Helices [My Copy] Journal of the American Chemical Society, Vol. 120, No. 37. (23 September 1998), pp. 9401-9409. by J. Srinivasan, T. E. Cheatham, P. Cieplak, P. A. Kollman, D. A. Case posted to interactions mmpbsa molecular-dynamics by bmduggan on 2008-10-23 18:06:55 as along with 2 people onufriev Elena_Zubova

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nmr	75
molecular-dynamics	60
tissuefactor	34
factorvii	29
relaxation	27
factorx	27
replication-fork	25
coagulation	24
interactions	24
review	20
spombe	17
napc2	16
crystal-structure	16
disulfide	14
thrombosis	14
cancer	14
expression	14
rna	13
sampling	10
nap5	9
swi1	8
sphingolipid	7
automated-assignment	7
equations	7
swi3	6
allostery	6
structure-prediction	6
mrc1	5
mmpbsa	5
mcm	5
rosetta	5
multicopy	5
inhibitor	5
tof1	5
scerevisiae	5
sequence-analysis	5
tipin	5
tim	5
csm3	4
std	4
model-free-approach	4
mat1	4
docking	4
inclusion-bodies	4
hsk1	3
cdc45	3
accelerated	3
thrombin	3
pulse-sequence	3
solution-structure	3
gins	3
convergence	3
factorix	3
protein-engineering	3
hirudin	3
protein_dynamics	3
protein_phosphatase-1	2
haddock	2
screening	2
protein-ligand	2
thermodynamic-integration	2
tip4p	2
targeted	2
ff99sb	2
temperature-coefficients	2
rad53	2
structure-determination	2
nap6	2
breast	2
phosphatidic_acid	2
trosy	2
tfe	1
protein-design	1
pseudomonas	1
ixolaris	1
tfpi	1
aceap1	1
par-2	1
ceramidase	1
rpa70	1
modeller	1
ramachandran	1
diffusion	1
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protein_phosphatase-2	1
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itc	1
shake	1
napc4	1
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design	1
apoptosis	1
serine-palmitoyltransferase	1
solution_structure	1
bicelles	1
phage	1
ceramide	1
spr	1
rotamers	1
tandem-affinity-purification	1
csi	1

bmduggan's molecular-dynamics [60 articles] Export Sort

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