barry's bd_simulation [38 articles] Export

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	Single molecule imaging reveals differences in microtubule track selection between Kinesin motors. [My Copy] PLoS biology, Vol. 7, No. 10. (October 2009) by Dawen Cai, Dyke P. McEwen, Jeffery R. Martens, Edgar Meyhofer, Kristen J. Verhey posted to mts molecular_motors kinesin bd_simulation by barry on 2009-10-15 18:11:23 as
	Graph-theoretical identification of dissociation pathways on free energy landscapes of biomolecular interaction [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Ling Wang, Boris Stumm, Volkhard Helms posted to bd_simulation by barry on 2009-09-04 00:39:27 as along with 2 people and 1 group anuragsethi sobolevnrm McCammon
	Association rate constants of ras-effector interactions are evolutionarily conserved. [My Copy] PLoS computational biology, Vol. 4, No. 12. (December 2008) by C. Kiel, D. Aydin, L. Serrano posted to bd_simulation ras by barry on 2009-06-17 01:04:18 as along with 2 people ras chad_davis
	Individual Rate Constants for the Interaction of Ras Proteins with GTPase-Activating Proteins Determined by Fluorescence Spectroscopy [My Copy] Biochemistry, Vol. 36, No. 15. (1 April 1997), pp. 4535-4541. by Mohammad R. Ahmadian, Ulrike Hoffmann, Roger S. Goody, Alfred Wittinghofer posted to bd_simulation ras by barry on 2009-06-17 00:48:36 as along with 1 person ras
	Simulating the electrostatic guidance of the vectorial translocations in hexameric helicases and translocases [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 18. (5 May 2009), pp. 7449-7454. by Hanbin Liu, Yemin Shi, Xiaojiang S. Chen, Arieh Warshel posted to bd_simulation dna_motor electrostatics by barry on 2009-05-21 04:03:23 as along with 1 person and 2 groups sobolevnrm McCammon baker-group
	Brownian search-and-catch mechanism for myosin-VI steps [My Copy] Nat Chem Biol, Vol. 5, No. 6. (June 2009), pp. 403-405. by Mitsuhiro Iwaki, Atsuko H. Iwane, Tetsuya Shimokawa, Roger Cooke, Toshio Yanagida posted to bd_simulation molecular_motors myosin by barry on 2009-05-20 01:15:02 as
	Species dependence of enzyme-substrate encounter rates for triose phosphate isomerases [My Copy] Proteins, Vol. 31, No. 4. (1998), pp. 406-16. by R. C. Wade, R. R. Gabdoulline, B. A. Luty posted to bd_simulation electrostatics by barry on 2009-05-16 23:36:41 as along with 1 person and 1 group sobolevnrm baker-group
	Diffusive reaction rates from Brownian dynamics simulations - replacing the outer cutoff surface by an analytical treatment [My Copy] Journal of Chemical Physics, Vol. 97, No. 8. (1992), pp. 5682-5686. by B. A. Luty, J. A. Mccammon, H. X. Zhou posted to bd_simulation by barry on 2009-05-16 23:33:03 as along with 1 person and 1 group sobolevnrm baker-group
	Identification of a strong binding site for kinesin on the microtubule using mutant analysis of tubulin [My Copy] The EMBO Journal, Vol. aop, No. current. (23 November 2006) by Seiichi Uchimura, Yusuke Oguchi, Miho Katsuki, et al.Takeo Usui, Hiroyuki Osada, Jun-Ichi Nikawa, Shin'ichi Ishiwata, Etsuko Muto posted to bd_simulation kinesin molecular_motors tubulin by barry on 2009-05-13 21:44:38 as along with 1 group McCammon
	Fundamental Aspects of Protein−Protein Association Kinetics [My Copy] Chemical Reviews, Vol. 109, No. 3. (11 March 2009), pp. 839-860. by G. Schreiber, G. Haran, H. X. Zhou posted to bd_simulation protein_protein by barry on 2009-04-21 08:24:42 as along with 10 people and 2 groups anuragsethi sunhwan jmccammon sobolevnrm willard kafuitay carlosjavierna sschurer hadesnumb paulschlesinger McCammon baker-group
	Protein Sliding along DNA: Dynamics and Structural Characterization [My Copy] Journal of Molecular Biology, Vol. 385, No. 4. (30 January 2009), pp. 1087-1097. by O. Givaty, Y. Levy posted to bd_simulation protein_dna by barry on 2009-03-25 21:27:28 as along with 2 people and 1 group sobolevnrm reyez baker-group
	Brownian dynamics simulation of diffusion-influenced bimolecular reactions [My Copy] The Journal of Chemical Physics, Vol. 80, No. 4. (1984), pp. 1517-1524. by Scott H. Northrup, Stuart A. Allison, Andrew J. Mccammon posted to bd_simulation by barry on 2009-03-20 22:42:38 as along with 3 people choonpeng stephenbond Martin8223
	Diffusive reaction rates from Brownian dynamics simulations: Replacing the outer cutoff surface by an analytical treatment [My Copy] The Journal of Chemical Physics, Vol. 97, No. 8. (1992), pp. 5682-5686. by Brock A. Luty, Andrew J. Mccammon, Huan X. Zhou posted to bd_simulation by barry on 2009-03-20 22:40:03 as
	Dynamics of protein-protein encounter: A Langevin equation approach with reaction patches [My Copy] The Journal of Chemical Physics, Vol. 129, No. 15. (2008) by Jakob Schluttig, Denitsa Alamanova, Volkhard Helms, Ulrich S. Schwarz posted to bd_simulation coarse_grain by barry on 2009-03-17 19:01:55 as along with 3 people and 2 groups anuragsethi sobolevnrm jmccammon baker-group McCammon
	Striking Effects of Hydrodynamic Interactions on the Simulated Diffusion and Folding of Proteins [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 2. (10 February 2009), pp. 242-256. by Tamara Frembgen-Kesner, Adrian H. Elcock posted to bd_simulation go_model hydrodynamics by barry on 2009-03-17 18:56:43 as along with 2 people and 2 groups sobolevnrm jmccammon baker-group McCammon
	Prediction of Protein-Protein Association Rates from a Transition-State Theory [My Copy] Structure, Vol. 15, No. 2. (February 2007), pp. 215-224. by R. Alsallaq, H. Zhou posted to bd_simulation electrostatics protein_protein by barry on 2009-03-13 18:41:53 as along with 2 people and 2 groups apaydin flbarroso structural_bioinformatics McCammon
	Electrostatic rate enhancement and transient complex of protein-protein association [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 71, No. 1. (11 October 2008), pp. 320-335. by Ramzi Alsallaq, Huan-Xiang Zhou posted to bd_simulation electrostatics by barry on 2009-03-13 18:19:26 as along with 2 people and 3 groups bicko sobolevnrm structural_bioinformatics McCammon baker-group
	The diffusive interaction of microtubule binding proteins [My Copy] Current Opinion in Cell Biology, Vol. 21, No. 1. (February 2009), pp. 68-73. by Jeremy R. Cooper, Linda Wordeman posted to bd_simulation molecular_motors mts review by barry on 2009-03-12 18:31:43 as along with 1 group McCammon
	Association of Cytochrome c with Membrane-Bound Cytochrome c Oxidase Proceeds Parallel to the Membrane Rather Than in Bulk Solution [My Copy] Biophysical Journal, Vol. 96, No. 5. (04 March 2009), pp. 1721-1732. by Alexander Spaar, Dagmar Flöck, Volkhard Helms posted to bd_simulation by barry on 2009-03-05 00:49:19 as along with 1 person paulschlesinger
	Free Energy Landscape of Protein−Protein Encounter Resulting from Brownian Dynamics Simulations of Barnase:Barstar [My Copy] Journal of Chemical Theory and Computation, Vol. 1, No. 4. (1 July 2005), pp. 723-736. by Alexander Spaar, Volkhard Helms posted to bd_simulation by barry on 2009-03-05 00:43:54 as
	Diffusional Encounter of Barnase and Barstar [My Copy] Biophys. J., Vol. 90, No. 6. (15 March 2006), pp. 1913-1924. by Alexander Spaar, Christian Dammer, Razif R. Gabdoulline, Rebecca C. Wade, Volkhard Helms posted to bd_simulation clustering by barry on 2009-03-05 00:43:04 as along with 2 people mikaellund Martin8223
	Electrostatically optimized Ras-binding Ral guanine dissociation stimulator mutants increase the rate of association by stabilizing the encounter complex. [My Copy] Proc Natl Acad Sci U S A, Vol. 101, No. 25. (22 June 2004), pp. 9223-9228. by C. Kiel, T. Selzer, Y. Shaul, G. Schreiber, C. Herrmann posted to ras protein_protein electrostatics bd_simulation by barry on 2007-01-16 23:20:45 as along with 2 groups structural_bioinformatics Bioinformatics
	Simulation methods for protein structure fluctuations. [My Copy] Biopolymers, Vol. 19, No. 5. (May 1980), pp. 1001-1016. by S. H. Northrup, J. A. McCammon posted to bd_simulation md_simulation review by barry on 2005-10-11 23:35:50 as along with 1 person and 2 groups lyongu structural_bioinformatics Bioinformatics
	Repulsive interactions between polar and apolar atoms in globular proteins. [My Copy] J Mol Biol, Vol. 151, No. 1. (5 September 1981), pp. 199-202. by B. Mao, M. R. Pear, J. A. McCammon, S. H. Northrup posted to bd_simulation electrostatics review by barry on 2005-10-11 23:35:20 as along with 2 groups structural_bioinformatics Bioinformatics
	Gated binding of ligands to proteins. [My Copy] Nature, Vol. 293, No. 5830. (24 September 1981), pp. 316-317. by J. A. McCammon, S. H. Northrup posted to bd_simulation review by barry on 2005-10-11 23:34:45 as along with 2 groups structural_bioinformatics Bioinformatics
	Simulation of biomolecular diffusion and complex formation. [My Copy] Biophys J, Vol. 49, No. 1. (January 1986), pp. 167-175. by S. A. Allison, S. H. Northrup, J. A. McCammon posted to bd_simulation electrostatics by barry on 2005-10-11 23:33:30 as along with 1 person and 2 groups lyongu structural_bioinformatics Bioinformatics
	Brownian simulation of protein association and reaction [My Copy] International Journal of Quantum Chemistry, Vol. 38, No. S17., pp. 55-71. by Scott H. Northrup, Robert G. Herbert posted to bd_simulation electrostatics review by barry on 2005-10-11 23:33:07 as along with 1 person and 2 groups lyongu structural_bioinformatics Bioinformatics
	Brownian dynamics simulation of protein association. [My Copy] J Comput Aided Mol Des, Vol. 1, No. 4. (January 1988), pp. 291-311. by S. H. Northrup, J. A. Luton, J. O. Boles, J. C. Reynolds posted to bd_simulation electrostatics review by barry on 2005-10-11 23:30:13 as along with 2 groups structural_bioinformatics Bioinformatics
	Brownian dynamics of cytochrome c and cytochrome c peroxidase association. [My Copy] Science, Vol. 241, No. 4861. (1 July 1988), pp. 67-70. by S. H. Northrup, J. O. Boles, J. C. Reynolds posted to bd_simulation electrostatics by barry on 2005-10-11 23:29:50 as along with 2 groups structural_bioinformatics Bioinformatics
	Experimental and theoretical analysis of the interaction between cytochrome c and cytochrome b5. [My Copy] J Bioenerg Biomembr, Vol. 27, No. 3. (June 1995), pp. 311-330. by A. G. Mauk, M. R. Mauk, G. R. Moore, S. H. Northrup posted to bd_simulation electrostatics by barry on 2005-10-11 23:28:22 as along with 2 groups structural_bioinformatics Bioinformatics
	Dynamics of protein-protein docking: cytochrome c and cytochrome c peroxidase revisited. [My Copy] J Biomol Struct Dyn, Vol. 16, No. 2. (October 1998), pp. 413-424. by G. Castro, C. A. Boswell, S. H. Northrup posted to bd_simulation electrostatics by barry on 2005-10-11 23:27:59 as along with 2 groups structural_bioinformatics Bioinformatics
	Kinetics of protein-protein association explained by Brownian dynamics computer simulation. [My Copy] Proc Natl Acad Sci U S A, Vol. 89, No. 8. (15 April 1992), pp. 3338-3342. by S. H. Northrup, H. P. Erickson posted to bd_simulation bioinf_methods electrostatics by barry on 2005-10-11 23:23:18 as along with 2 groups structural_bioinformatics Bioinformatics
	Simulation of electrostatic effects in Fab-antigen complex formation. [My Copy] Eur J Biochem, Vol. 267, No. 15. (August 2000), pp. 4861-4869. by F. Fogolari, R. Ugolini, H. Molinari, P. Viglino, G. Esposito posted to bd_simulation electrostatics by barry on 2005-10-11 23:06:04 as along with 2 groups structural_bioinformatics Bioinformatics
	Brownian Dynamics Simulation of Protein-Protein Diffusional Encounter [My Copy] Methods, Vol. 14, No. 3. (March 1998), pp. 329-341. by Razif R. Gabdoulline, Rebecca C. Wade posted to bd_simulation bioinf_methods electrostatics by barry on 2005-10-11 03:54:33 as along with 2 people and 2 groups m_j Martin8223 structural_bioinformatics Bioinformatics
	Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program [My Copy] Computer Physics Communications, Vol. 91, No. 1-3. (02 September 1995), pp. 57-95. by J. Madura posted to bd_simulation bioinf_methods electrostatics by barry on 2005-10-11 02:25:41 as along with 2 people and 2 groups flbarroso sim82 structural_bioinformatics Bioinformatics
	Computer simulation of protein-protein association kinetics: acetylcholinesterase-fasciculin. [My Copy] J Mol Biol, Vol. 291, No. 1. (6 August 1999), pp. 149-162. by A. H. Elcock, R. R. Gabdoulline, R. C. Wade, J. A. McCammon posted to bd_simulation bioinf_methods electrostatics by barry on 2005-10-11 02:13:35 as along with 3 people and 2 groups dfgreen mikaellund Martin8223 structural_bioinformatics Bioinformatics
	Electrostatic analysis and Brownian dynamics simulation of the association of plastocyanin and cytochrome f. [My Copy] Biophys J, Vol. 81, No. 6. (December 2001), pp. 3090-3104. by F. De Rienzo, R. R. Gabdoulline, M. C. Menziani, P. G. De Benedetti, R. C. Wade posted to bd_simulation bioinf_methods electrostatics by barry on 2005-10-11 02:09:35 as along with 2 groups structural_bioinformatics Bioinformatics
	Model describing the biased Brownian movement of myosin [My Copy] Proceedings of the Japan Academy, Series B (Physical and Biological Sciences), Vol. 79, No. 1. (2003), pp. 9-14. by S. Esaki, Y. Ishii, T. Yanagida posted to bd_simulation molecular_motors myosin by barry on 2005-09-20 19:04:07 as along with 1 person and 2 groups melting structural_bioinformatics Bioinformatics

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protein_structure	278
molecular_motors	190
review	190
kinesin	145
protein_dynamics	132
md_simulation	93
protein_sequence	83
protein_protein	77
bioinf_methods	76
protein_evolution	69
protein_design	65
nma	50
structure_comparison	46
structural_bioinformatics	45
cytoskeleton	44
tubulin	42
allosteric	39
bd_simulation	38
myosin	37
electrostatics	34
dynein	29
pca	29
ctbp	27
drug_design	26
sequence_comparison	24
eg5	23
ras	23
correlated_mutations	22
nmr	21
motor_model	20
kinases	19
protein_folding	19
domain_motions	18
monastrol	18
g_proteins	17
clustering	16
docking	16
bioinformatics	15
coarse_grain	15
core_structure	15
ntpases	14
correlated_motions	13
networks	13
protein_ligand	13
career	12
comparative_model	12
p-loop	12
contacts	11
core_residues	11
hbond	11
fold_space	10
free_energy	9
general	9
gotit	9
mts	9
aaa	8
mine	8
pdz	8
protein_fragments	8
protein_packing	8
sca	8
small_world	8
torsion_angles	8
transcription_factor	8
cargo_attachment	7
conformational_selection	7
dehydron	7
mitosis	7
nachr	7
r	7
cell_cycle_inhibitors	6
cryo_em	6
distance_matrices	6
drug_discovery	6
ion_channels	6
actin	5
binding	5
inhibitor_design	5
microarrays	5
mutants	5
phylogeny	5
replica_exchange	5
adk	4
allostery	4
cancer	4
hsp90	4
myovi	4
ncd	4
ribosome	4
smd	4
accelerated_md	3
adh	3
alex	3
cath	3
chagas	3
coarse-grained	3
dynamic_similarity	3
function_prediction	3
genomic_context	3
gpcr	3
groel	3
guide	3
ion_pairs	3
itc	3
kif1a	3
kin13	3
kin14_kar3	3
membranes	3
myov	3
nadp	3
neck_linker	3
poster	3
protein_function	3
protein-ligand	3
protein-protein	3
residue_annotation	3
server	3
structure_refinement	3
svm	3
swi-swii	3
test	3
tropical_diseases	3
achr	2
advice	2
amber	2
arf	2
bayesian_classifiers	2
beta_sheet	2
brownian_dynamics	2
clipx	2
coiled_coil	2
disorder	2
dna_motor	2
documentation	2
epr	2
fret-fiona	2
go_model	2
graph	2
helix_helix	2
hinge_motion	2
ikk	2
interaction_maps	2
journal_club	2
kin8	2
kini	2
ksca	2
malaria	2
membrane_proteins	2
mm-pbsa	2
motor_mode	2
neural_net	2
nfkb	2
ntp	2
nucleotide_analogues	2
pka	2
pmf	2
protein_dna	2
pxdls	2
rab	2
rho	2
sampling	2
sequence_motif	2
solvation	2
solvent	2
structure_determination	2
student	2
subfamily	2
time_series_analysis	2
titration	2
aaindex	1
abc	1
afm	1
afp	1
alanine_scanning	1
alpha_actinin	1
alzheimers	1
antibodys	1
antiviral_drugs	1
arp3	1
bacteriorhodopsin	1
book2get	1
bpti	1
catalytic_mechanism	1
cftr	1
chip-chip	1
chromokinesin	1
cis_trans	1
citrate_synthase	1
cloud_computing	1
coevolution	1
comparative_genomics	1
complexity	1
conformational_search	1
convergent_evolution	1
cracking	1
crystal_packing	1
decision_trees	1
diffusion	1
directed_evolution	1
discussion_free_energy	1
docking_refinement	1
domain_swapping	1
doublecortin	1
ef-g	1
ef-tu	1
em	1
epitopes	1
essay	1
f1atpase	1
fad	1
farnesyltransferase	1
fdh	1
ff99sb	1
flagella	1
flagellar_motor	1
flu	1
fold	1
for_ana	1
force_field	1
fret	1
ftsz	1
funding	1
gaba	1
gdh	1
gene_duplication	1
gene_expression	1
gene_finding	1
gene_ontology	1
genome	1
gfp	1
gpus	1
helicases	1
hiv	1
hiv_integrase	1
hiv_rt	1
hoh	1
hot_spots	1
hsp104	1
hsp70	1
hydrodynamics	1
hydrophobic	1
immunology	1
imp_dehydrogenase	1
ion_channel	1
jc	1
kar3	1
kinesin_neck	1
kinesin_tail	1
kinetics	1
kinetochores	1
kin_loop5	1
kin-mtl	1
landscapes	1
ldh	1
literature	1
loop_modeling	1
mcak	1
md	1
mdh	1
membrane	1
metadynamics	1
mg	1
mmp	1
molecular_moters	1
motor_cargo	1
multiscale	1
nad	1
nadh	1
nemo	1
nice_figure	1
pathways	1
pcna	1
pcp	1
pdb	1
perl	1
pgdh	1
phosphorylation	1
power_law	1
programming	1
proline	1
promoter_finding	1
promoter_identification	1
protein_annotation	1
protein_engineering	1
protein_stability	1
protein_strcture	1
protonation	1
ptms	1
qm	1
qm_mm	1
rabkinesin	1
rafts	1
ran	1
residue_effect	1
rna	1
rna_dynamics	1
rna_polymerase	1
roc	1
sas	1
scop	1
sequence_conservation	1
sequencing	1
sheer_motion	1
siginal_transduction	1
similarity	1
single_molecule	1
smallrna	1
sos	1
species_evolution	1
structural_genomics	1
structure_alignment	1
superamolecular	1
systems_biology	1
torsion	1
transition_state	1
tyrosine_kinase	1
tyrosine_phosphatases	1
ubiqutin	1
umbrella	1
virulence_factors	1
virus	1
wavelets	1
wham	1
wireing_digrams	1

barry's bd_simulation [38 articles] Export

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