cactus's md [39 articles] Export

Recent papers added to cactus's library classified by the tag md. You can also see everyone's md.

	Friction laws at the nanoscale [My Copy] Nature, Vol. 457, No. 7233. (26 February 2009), pp. 1116-1119. by Yifei Mo, Kevin T. Turner, Izabela Szlufarska posted to clip2 md physics simulation by cactus on 2009-03-11 08:45:11 as along with 1 person pick600
	Stabilizing effect of knots on proteins [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 50. (16 December 2008), pp. 19714-19719. by Joanna I. Sułkowska, Piotr Sułkowski, P. Szymczak, Marek Cieplak posted to md protein simulation by cactus on 2008-12-18 07:23:18 as along with 3 people sunrise melting itmeson
	Nucleotide Effects on the Structure and Dynamics of Actin. [My Copy] Biophys J (25 May 2007) by Xiange Zheng, Karthikeyan Diraviyam, David Sept posted to actin fullatom md protein by cactus on 2008-11-07 08:20:08 as along with 2 people jstajic choonpeng
	Allostery of actin filaments: molecular dynamics simulations and coarse-grained analysis. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 37. (13 September 2005), pp. 13111-13116. by J. W. Chu, G. A. Voth posted to actin coarse-grained filament fullatom md protein by cactus on 2008-11-07 07:48:40 as along with 2 people BragilMassoud choonpeng
	Nanopore–Protein Interactions Dramatically Alter Stability and Yield of the Native State in Restricted Spaces [My Copy] Journal of Molecular Biology, Vol. 357, No. 2. (24 March 2006), pp. 632-643. by M. Cheung, D. Thirumalai posted to chaperonin coarse-grained confinement md simulation by cactus on 2008-10-07 08:39:21 as
	Assembly and Kinetic Folding Pathways of a Tetrameric beta-Sheet Complex: Molecular Dynamics Simulations on Simplified Off-Lattice Protein Models [My Copy] Biophys. J., Vol. 86, No. 1. (1 January 2004), pp. 31-49. by Hyunbum Jang, Carol K. Hall, Yaoqi Zhou posted to amyloid coarse-grained for_ref md oligomer simulation by cactus on 2008-10-07 07:28:49 as
	Molecular crowding enhances native state stability and refolding rates of globular proteins [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 13. (29 March 2005), pp. 4753-4758. by Margaret S. Cheung, Dmitri Klimov, D. Thirumalai posted to coarse-grained crowding for_ref md simulation by cactus on 2008-10-02 07:00:45 as along with 2 people ras sikorski
	The influence of macromolecular crowding on HIV-1 protease internal dynamics. [My Copy] Journal of the American Chemical Society, Vol. 128, No. 18. (10 May 2006), pp. 6006-6007. by D. D. Minh, C. E. Chang, J. Trylska, V. Tozzini, J. A. McCammon posted to coarse-grained crowding for_ref md simulation by cactus on 2008-10-01 07:56:42 as
	Protein folding under confinement: A role for solvent [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 25. (19 June 2007), pp. 10430-10434. by Del Lucent, V. Vishal, Vijay S. Pande posted to confinement for_ref fullatom md simulation by cactus on 2008-09-29 11:12:32 as along with 4 people carlosjavierna melting cjeans rph
	Structural transitions of confined model proteins: molecular dynamics simulation and experimental validation. [My Copy] Biophys J, Vol. 90, No. 9. (1 May 2006), pp. 3224-3238. by D. Lu, Z. Liu, J. Wu posted to coarse-grained confinement experiment md simulation by cactus on 2008-09-29 09:07:42 as along with 1 person allmensch
	Minimalist Protein Model as a Diagnostic Tool for Misfolding and Aggregation [My Copy] Journal of Molecular Biology, Vol. 363, No. 1. (13 October 2006), pp. 297-308. by Silvina Matysiak, Cecilia Clementi posted to folding md model protein by cactus on 2008-04-18 12:26:33 as
	Mechanochemical Coupling in the Myosin Motor Domain. II. Analysis of Critical Residues [My Copy] PLoS Comput Biol, Vol. 3, No. 2. (16 February 2007), e23. by Haibo Yu, Liang Ma, Yang Yang, Qiang Cui posted to analysis md motor myosin normal-mode by cactus on 2008-02-27 07:15:45 as along with 1 person Diego_Prada
	Mechanochemical Coupling in the Myosin Motor Domain. I. Insights from Equilibrium Active-Site Simulations [My Copy] PLoS Computational Biology, Vol. 3, No. 2. (1 February 2007), e21. by Haibo Yu, Liang Ma, Yang Yang, Qiang Cui posted to fullatom md motor myosin qmmm by cactus on 2008-02-27 07:04:00 as
	Force Generation in Kinesin Hinges on Cover-Neck Bundle Formation [My Copy] Structure, Vol. 16, No. 1. (8 January 2008), pp. 62-71. by Wonmuk Hwang, Matthew J. Lang, Martin Karplus posted to fullatom kinesin md motor by cactus on 2008-02-20 07:45:41 as
	How subunit coupling produces the gamma-subunit rotary motion in F1-ATPase [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 4. (29 January 2008), pp. 1192-1197. by Jingzhi Pu, Martin Karplus posted to coarse-grained elastic-network f1-atpase md by cactus on 2008-02-13 10:01:05 as
	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 md method structural_change by cactus on 2008-02-13 09:56:52 as along with 2 people Diego_Prada LamBras
	Allosteric effects in the marginally stable von Hippel-Lindau tumor suppressor protein and allostery-based rescue mutant design [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 3. (22 January 2008), pp. 901-906. by Jin Liu, Ruth Nussinov posted to allostery design fullatom md mutation by cactus on 2008-02-13 07:31:01 as along with 1 person and 1 group sobolevnrm baker-group
	Molecular crowding enhances native structure and stability of alpha/ protein flavodoxin [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 48. (27 November 2007), pp. 18976-18981. by Loren Stagg, Shao-Qing Zhang, Margaret S. Cheung, Pernilla Wittung-Stafshede posted to crowding experiment md stability by cactus on 2008-01-11 10:28:12 as along with 2 people saunders min013
	Intrinsic motions along an enzymatic reaction trajectory. [My Copy] Nature, Vol. 450, No. 7171. (6 December 2007), pp. 838-844. by Katherine A. Henzler-Wildman, Vu Thai, Ming Lei, et al.Maria Ott, Magnus Wolf-Watz, Tim Fenn, Ed Pozharski, Mark A. Wilson, Gregory A. Petsko, Martin Karplus, Christian G. Hübner, Dorothee Kern posted to adk enzyme fret function md nmr normal-mode protein structural_change by cactus on 2008-01-11 06:46:50 as along with 12 people and 1 group saravan ahmetbakan xdeupi ubcg08l ruvido barry aqeel ebeutler sobolevnrm paulschlesinger jlh64 yalexeev baker-group
	Theoretical Studies of the ATP Hydrolysis Mechanism of Myosin [My Copy] Biophys. J., Vol. 81, No. 5. (1 November 2001), pp. 2786-2794. by Noriaki Okimoto, Kazunori Yamanaka, Junko Ueno, Masayuki Hata, Tyuji Hoshino, Minoru Tsuda posted to md motor myosin qmmm by cactus on 2007-12-06 13:29:05 as
	On the Mechanism of ATP Hydrolysis in F1-ATPase [My Copy] Biophys. J., Vol. 85, No. 4. (1 October 2003), pp. 2253-2266. by Markus Dittrich, Shigehiko Hayashi, Klaus Schulten posted to f1-atpase md qmmm by cactus on 2007-12-06 13:26:38 as
	The Unbinding of ATP from F1-ATPase [My Copy] Biophys. J., Vol. 85, No. 2. (1 August 2003), pp. 695-706. by Iris Antes, David Chandler, Hongyun Wang, George Oster posted to clip f1-atpase fullatom ligand md by cactus on 2007-12-06 13:25:44 as
	Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 47. (20 November 2007), pp. 18496-18501. by Karunesh Arora, Charles L. Brooks posted to allostery binding free-energy fullatom ligand md structural_change by cactus on 2007-11-22 10:02:13 as along with 7 people and 2 groups xdeupi jrperillaj barry allmensch sobolevnrm jlh64 karunesh structural_bioinformatics baker-group
	Mutations as trapdoors to two competing native conformations of the Rop-dimer [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 45. (6 November 2007), pp. 17674-17679. by Alexander Schug, Paul C. Whitford, Yaakov Levy, Jose N. Onuchic posted to coarse-grained md multi-basin structural_change by cactus on 2007-11-22 09:17:07 as
	Mechanical control of the directional stepping dynamics of the kinesin motor [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 44. (30 October 2007), pp. 17382-17387. by Changbong Hyeon, Jose N. Onuchic posted to 2-heads coarse-grained kinesin md motor by cactus on 2007-11-22 09:03:19 as along with 1 person softsimu
	From the Cover: Hierarchies, multiple energy barriers, and robustness govern the fracture mechanics of alpha-helical and beta-sheet protein domains [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 42. (16 October 2007), pp. 16410-16415. by Theodor Ackbarow, Xuefeng Chen, Sinan Keten, Markus J. Buehler posted to clip2 force fullatom md stability by cactus on 2007-11-22 08:03:08 as along with 1 person choonpeng
	A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 40. (2 October 2007), pp. 15711-15716. by Amit Ghosh, Saraswathi Vishveshwara posted to analysis correlation dynamics fullatom md by cactus on 2007-11-20 11:41:30 as along with 3 people and 1 group zwang sobolevnrm phoenixzxl baker-group
	The Folding Energy Landscape of the Dimerization Domain of Escherichia coli Trp Repressor: A Joint Experimental and Theoretical Investigation [My Copy] Journal of Molecular Biology, Vol. 363, No. 1. (13 October 2006), pp. 262-278. by Robert B. Simler, Yaakov Levy, Jose N. Onuchic, Robert C. Matthews posted to dimerization md by cactus on 2007-10-24 11:17:26 as
	Protein Oligomerization Through Domain Swapping: Role of Inter-molecular Interactions and Protein Concentration [My Copy] Journal of Molecular Biology, Vol. 352, No. 1. (9 September 2005), pp. 202-211. by Sichun Yang, Herbert Levine, Jose N. Onuchic posted to dimer domain_swapping md by cactus on 2007-10-23 10:56:35 as
	A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes. [My Copy] Journal of molecular biology, Vol. 346, No. 4. (4 March 2005), pp. 1121-1145. by Yaakov Levy, Samuel S. Cho, José N. Onuchic, Peter G. Wolynes posted to dimer domain_swapping md by cactus on 2007-10-23 10:10:44 as
	Open interface and large quaternary structure movements in 3D domain swapped proteins: insights from molecular dynamics simulations of the C-terminal swapped dimer of ribonuclease A. [My Copy] Biophys J, Vol. 88, No. 3. (March 2005), pp. 2003-2012. by A. Merlino, M. A. Ceruso, L. Vitagliano, L. Mazzarella posted to dimer domain_swapping fullatom md rnase_a by cactus on 2007-10-12 09:18:19 as
	In silico study of amyloid beta-protein folding and oligomerization. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, No. 50. (14 December 2004), pp. 17345-17350. by B. Urbanc, L. Cruz, S. Yun, et al.S. V. Buldyrev, G. Bitan, D. B. Teplow, H. E. Stanley posted to a-beta amyloid md model by cactus on 2007-10-02 11:57:43 as along with 2 people flbarroso chiufanlee
	Molecular Dynamics Simulation of Amyloid β Dimer Formation [My Copy] Biophysical Journal, Vol. 87, No. 4. (1 October 2004), pp. 2310-2321. by B. Urbanc, L. Cruz, F. Ding, et al.D. Sammond, S. Khare, S. Buldyrev, H. Stanley, N. Dokholyan posted to a-beta amyloid md model by cactus on 2007-10-02 11:50:11 as along with 3 people zfekete flbarroso Diego_Prada
	Atomic structures of peptide self-assembly mimics [My Copy] PNAS, Vol. 103, No. 47. (21 November 2006), pp. 17753-17758. by Koki Makabe, Dan Mcelheny, Valentia Tereshko, et al.Aaron Hilyard, Grzegorz Gawlak, Shude Yan, Akiko Koide, Shohei Koide posted to amyloid md model by cactus on 2007-08-13 11:42:03 as
	Molecular Dynamics Analysis of Structural Factors Influencing Back Door Pi Release in Myosin [My Copy] Biophys. J., Vol. 86, No. 6. (1 June 2004), pp. 3794-3803. by David J. Lawson, Edward Pate, Ivan Rayment, Ralph G. Yount posted to fullatom md motor myosin pi by cactus on 2007-06-06 18:18:15 as
	Coupling between allosteric transitions in GroEL and assisted folding of a substrate protein [My Copy] PNAS, Vol. 104, No. 21. (22 May 2007), pp. 8803-8808. by George Stan, George H. Lorimer, D. Thirumalai, Bernard R. Brooks posted to chaperonin groel md by cactus on 2007-05-24 08:41:05 as along with 1 person rph
	Hydrophobic Cooperativity as a Mechanism for Amyloid Nucleation [My Copy] Journal of Molecular Biology, Vol. 368, No. 3. (4 May 2007), pp. 894-901. by Jr Hills, Brooks posted to amyloid fullatom md model by cactus on 2007-05-07 10:20:16 as
	The Principal Motions Involved in the Coupling Mechanism of the Recovery Stroke of the Myosin Motor [My Copy] Journal of Molecular Biology, Vol. 367, No. 2. (23 March 2007), pp. 591-602. by Sidonia Mesentean, Sampath Koppole, Jeremy C. Smith, Stefan Fischer posted to md motor myosin by cactus on 2007-05-07 09:54:01 as
	The Structure of the Alzheimer Amyloid [beta] 10-35 Peptide Probed through Replica-Exchange Molecular Dynamics Simulations in Explicit Solvent [My Copy] Journal of Molecular Biology, Vol. 366, No. 1. (9 February 2007), pp. 275-285. by Andrij Baumketner, Joan-Emma Shea posted to a-beta amyloid fullatom md by cactus on 2007-05-07 08:53:11 as along with 1 person carlescorbi

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experiment	141
protein	100
motor	87
myosin	74
clip2	55
structure	50
review	41
md	39
amyloid	38
xray-crystal-structure	33
allostery	29
clip	25
nmr	25
folding	24
kinesin	23
structural_change	21
model	18
simulation	18
analysis	17
dimer	17
stability	17
crowding	16
fullatom	16
binding	15
intrinsic_disorder	14
mutation	14
rna	14
theory	14
network	13
coarse-grained	11
fluorescent	11
kinetics	11
muscle	11
ribosome	11
chaperonin	10
confinement	10
domain_swapping	10
protein-protein_interaction	10
a-beta	9
cell	9
dimerization	9
evolution	9
fret	9
strain	9
actin	8
em	8
enzyme	8
f1-atpase	8
for_ref	8
inhibitor	8
mc	8
pi	8
chaperone	7
groel	7
ligand	7
oligomer	7
single_molecule	7
channel	5
design	5
diffusion	5
entropy	5
fiber	5
function	5
lambdacro	5
mutant	5
physics	5
qmmm	5
xray-diffraction	5
dynein	4
free-energy	4
gene_expression	4
isoform	4
method	4
news-and-view	4
polymerization	4
prion	4
ref-pc	4
regulation	4
seca	4
visualization	4
aaa	3
adp	3
alignment	3
calorimetry	3
computation	3
ecology	3
in_vivo	3
microtubule	3
normal-mode	3
pattern_formation	3
processivity	3
sequence	3
2-heads	2
adaptation	2
adk	2
afm	2
atp	2
biology	2
chamical_reaction	2
circadeian	2
database	2
dynamics	2
ecoli	2
elastic-network	2
energetics	2
epr	2
filament	2
fluctuation	2
historical	2
homologue	2
interaction	2
lattice	2
nucleotide	2
pathway	2
prediction	2
protease	2
proteome	2
reaction	2
rnase_a	2
signal	2
statistical	2
stochastic	2
sup35	2
thermodynamics	2
trp	2
xray-scattering	2
aggregation	1
bioinformatics	1
brownian-dynamics	1
chaos	1
chemistry	1
cited	1
clpb	1
complex	1
correlation	1
dissociation	1
dna	1
dnak	1
dna-polymerase	1
domain	1
egfr	1
error	1
esr	1
estimate	1
fly-casting	1
foodweb	1
force	1
for_rev	1
fpt	1
frustration	1
fun	1
geometry	1
granular-material	1
growth	1
helicase	1
hybridization	1
hydration	1
inactivation	1
insulin	1
isomerize	1
language	1
light-chain	1
membrane	1
microglobulin	1
mine	1
modeling	1
molten_globule	1
mt	1
multi-basin	1
myosinv	1
nonequilibrium	1
o	1
packing	1
parasite	1
pca	1
phenotype	1
polar	1
population-dynamics	1
potential	1
preview	1
re	1
rna-polymerase	1
self_assembly	1
small	1
spin	1
splicing	1
stochastic_process	1
temperature	1
time_series	1
translocation	1
transport	1
unfolding	1

cactus's md [39 articles] Export

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