allmensch's library 609 articles Export

	The nature of protein folding pathways: The classical versus the new view [My Copy] Journal of Biomolecular NMR, Vol. 5, No. 2. (1 February 1995), pp. 103-109. by Robert L. Baldwin posted to trpzip proteinfolding by allmensch on 2009-11-19 13:37:35 as
	Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation [My Copy] Current Opinion in Structural Biology In Catalysis and regulation / Proteins, Vol. 17, No. 6. (December 2007), pp. 633-640. by Ivet Bahar, Chakra Chennubhotla, Dror Tobi posted to unfolded by allmensch on 2009-09-23 15:21:52 as along with 10 people and 4 groups jrperillaj barry aqeel ruvido cactus sobolevnrm jennifermbui higueruelo LamBras jmccammon structural_bioinformatics Bioinformatics baker-group McCammon
	ParaFrag—an approach for surface-based similarity comparison of molecular fragments [My Copy] Journal of Molecular Modeling, Vol. 14, No. 7. (31 July 2008), pp. 547-558. by Arjen-Joachim Jakobi, Harald Mauser, Timothy Clark posted to fluorobases by allmensch on 2009-09-17 08:27:36 as along with 1 person superpyrin
	Evaluating the Performance of the ff99SB Force Field Based on NMR Scalar Coupling Data [My Copy] Biophysical Journal, Vol. 97, No. 3. (05 August 2009), pp. 853-856. by Lauren Wickstrom, Asim Okur, Carlos Simmerling posted to lysozyme forcefield by allmensch on 2009-09-04 14:07:57 as
	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 lysozyme forcefield by allmensch on 2009-09-04 13:52:14 as along with 11 people and 1 group xdeupi agrossfield bmduggan r2s2 apaydin kiekyon Borelli idoerg sobolevnrm edws paulschlesinger baker-group
	Rescoring docking hit lists for model cavity sites: predictions and experimental testing. [My Copy] Journal of molecular biology, Vol. 377, No. 3. (28 March 2008), pp. 914-934. by Alan P. Graves, Devleena M. Shivakumar, Sarah E. Boyce, Matthew P. Jacobson, David A. Case, Brian K. Shoichet posted to usa ras docking by allmensch on 2009-09-02 13:23:09 as along with 1 person and 1 group sobolevnrm baker-group
	The molecular architecture of protein-protein binding sites. [My Copy] Current opinion in structural biology, Vol. 17, No. 1. (February 2007), pp. 67-76. by Dana Reichmann, Ofer Rahat, Mati Cohen, Hani Neuvirth, Gideon Schreiber posted to usa ras protprot by allmensch on 2009-09-02 13:19:18 as along with 6 people laurabailey bicko choonpeng hmk higueruelo marti
	Continuum Secondary Structure Captures Protein Flexibility [My Copy] Structure, Vol. 10, No. 2. (February 2002), pp. 175-184. by C. Andersen, A. Palmer, S. Brunak, B. Rost posted to trpzip strcuture secondary method dssp by allmensch on 2009-08-18 10:20:38 as
	DSSPcont: continuous secondary structure assignments for proteins [My Copy] Nucleic Acids Research (July 2003), pp. 3293-3295. by Phil Carter, Claus A. F. Andersen, Burkhard Rost posted to trpzip strcuture secondary method dssp by allmensch on 2009-08-18 10:18:36 as
	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 umbrellasampling trpzip kinase by allmensch on 2009-08-18 10:09:47 as along with 3 people bmduggan choonpeng ruvido
	Src Kinase Conformational Activation: Thermodynamics, Pathways, and Mechanisms [My Copy] PLoS Comput Biol, Vol. 4, No. 3. (28 March 2008), e1000047. by Sichun Yang, Benoît Roux posted to umbrellasampling trpzip kinase by allmensch on 2009-08-18 09:46:52 as along with 2 people iivanov bootsy
	Binding specificity of SH2 domains: insight from free energy simulations. [My Copy] Proteins, Vol. 74, No. 4. (2 March 2009), pp. 996-1007. by Wenxun Gan, Benoît Roux posted to umbrellasampling trpzip kinase by allmensch on 2009-08-18 09:35:42 as along with 2 people and 1 group jmccammon ibuch McCammon
	Autoinhibition and activation mechanisms of the Wiskott-Aldrich syndrome protein. [My Copy] Nature, Vol. 404, No. 6774. (9 March 2000), pp. 151-158. by A. S. Kim, L. T. Kakalis, N. Abdul-Manan, G. A. Liu, M. K. Rosen posted to trpzip kinase by allmensch on 2009-08-18 09:34:57 as along with 1 person djmonstermo
	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, Vol. 106, No. 10. (10 March 2009), pp. 3776-3781. by Sichun Yang, Nilesh K. Banavali, BenoÃ®t Roux posted to trpzip transitionstate by allmensch on 2009-08-18 09:31:40 as along with 7 people and 2 groups anuragsethi Diego_Prada bmduggan guhjy sobolevnrm barry jmccammon baker-group McCammon
	Configurational distribution of denatured phosphoglycerate kinase. [My Copy] Journal of molecular biology, Vol. 231, No. 3. (5 June 1993), pp. 840-848. by P. Calmettes, B. Roux, D. Durand, M. Desmadril, J. C. Smith posted to unfolded lysozyme by allmensch on 2009-08-18 09:28:27 as
	Reaction coordinates and rates from transition paths. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 19. (10 May 2005), pp. 6732-6737. by Robert B. Best, Gerhard Hummer posted to trpzip by allmensch on 2009-08-17 14:14:44 as along with 4 people apaydin bilab mtw jlh64
	Structural basis for the interaction of Ras with RalGDS. [My Copy] Nature structural biology, Vol. 5, No. 6. (June 1998), pp. 422-426. by L. Huang, F. Hofer, G. S. Martin, S. H. Kim posted to ras usa xray by allmensch on 2009-08-03 14:03:47 as
	Low-Lying Excited States of Proteins Revealed from Nonlinear Pressure Shifts in 1H and 15N NMR† [My Copy] Biochemistry, Vol. 40, No. 30. (1 July 2001), pp. 8665-8671. by Kazuyuki Akasaka, Hua Li posted to ras thr35 usa by allmensch on 2009-07-29 16:54:41 as
	High-pressure NMR study of the complex of a GTPase Rap1A with its effector RalGDS A conformational switch in RalGDS revealed from non-linear pressure shifts [My Copy] FEBS Letters, Vol. 506, No. 3. (12 October 2001), pp. 180-184. by K. Inoue posted to ras thr35 usa by allmensch on 2009-07-29 16:53:45 as
	c-Raf-1 RBD Associates with a Subset of Active v-H-Ras† [My Copy] Biochemistry, Vol. 39, No. 50. (1 December 2000), pp. 15603-15611. by Masha Fridman, Francesca Walker, Bruno Catimel, Teresa Domagala, Edouard Nice, Antony Burgess posted to ras thr35 usa by allmensch on 2009-07-29 16:51:33 as
	Thermodynamic and Kinetic Characterization of the Interaction between the Ras Binding Domain of AF6 and Members of the Ras Subfamily [My Copy] J. Biol. Chem., Vol. 274, No. 19. (7 May 1999), pp. 13556-13562. by Thomas Linnemann, Matthias Geyer, Birgit K. Jaitner, et al.Christoph Block, Hans R. Kalbitzer, Alfred Wittinghofer, Christian Herrmann posted to ras thr35 usa by allmensch on 2009-07-29 16:50:27 as
	Solution Structure of the Ras Binding Domain of the Protein Kinase Byr2 from Schizosaccharomyces pombe [My Copy] Structure, Vol. 9, No. 11. (November 2001), pp. 1029-1041. by Wolfram Gronwald, Fritz Huber, Petra Grünewald, et al.Michael Spörner, Sabine Wohlgemuth, Christian Herrmann, Hans R. Kalbitzer posted to ras thr35 usa by allmensch on 2009-07-29 16:48:57 as
	Conformational Transitions in p21ras and in Its Complexes with the Effector Protein Raf-RBD and the GTPase Activating Protein GAP† [My Copy] Biochemistry, Vol. 35, No. 32. (1 January 1996), pp. 10308-10320. by Matthias Geyer, Thomas Schweins, Christian Herrmann, Thomas Prisner, Alfred Wittinghofer, Hans R. Kalbitzer posted to ras thr35 usa by allmensch on 2009-07-29 16:47:09 as
	Dynamic properties of the Ras switch I region and its importance for binding to effectors. [My Copy] Proceedings of the National Academy of Sciences of the United States of America. , Vol. 98, No. 9. (24 April 2001), pp. 4944-4949. by M. Spoerner, C. Herrmann, I. R. Vetter, H. R. Kalbitzer, A. Wittinghofer posted to ras thr35 usa by allmensch on 2009-07-29 16:43:19 as along with 2 people laurabailey gloria
	Towards an Understanding of the Temperature/ Pressure Configurational and Free-Energy Landscape of Biomolecules [My Copy] Journal of Non Equilibrium Thermodynamics, Vol. 32 (February 2007), pp. 41-97. by R. Winter, D. Lopes, S. Grudzielanek, K. Vogtt posted to trpzip by allmensch on 2009-07-22 11:31:50 as
	Novel type of Ras effector interaction established between tumour suppressor NORE1A and Ras switch II [My Copy] The EMBO Journal, Vol. aop, No. current. (03 July 2008) by Benjamin Stieglitz, Christine Bee, Daniel Schwarz, et al.Ozkan Yildiz, Anna Moshnikova, Andrei Khokhlatchev, Christian Herrmann posted to ras usa by allmensch on 2009-06-26 16:53:51 as along with 1 person laurabailey
	Peptides containing a consensus Ras binding sequence from Raf-1 and theGTPase activating protein NF1 inhibit Ras function [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 93, No. 4. (20 February 1996), pp. 1577-1581. by G. J. Clark, J. K. Drugan, R. S. Terrell, et al.C. Bradham, C. J. Der, R. M. Bell, S. Campbell posted to ras usa by allmensch on 2009-06-26 16:45:17 as
	RAS inhibitors: potential for cancer therapeutics. [My Copy] Molecular medicine today, Vol. 6, No. 10. (October 2000), pp. 398-402. by Y. Kloog, A. D. Cox posted to ras usa by allmensch on 2009-06-26 16:38:48 as
	Specificity and mechanism of action of EHT 1864, a novel small molecule inhibitor of Rac family small GTPases. [My Copy] The Journal of biological chemistry, Vol. 282, No. 49. (7 December 2007), pp. 35666-35678. by A. Shutes, C. Onesto, V. Picard, B. Leblond, F. Schweighoffer, C. J. Der posted to drugdesign rac ras usa by allmensch on 2009-06-26 16:13:28 as
	Structure-function based design of small molecule inhibitors targeting Rho family GTPases. [My Copy] Curr Top Med Chem, Vol. 6, No. 11. (2006), pp. 1109-1116. by N. Nassar, J. Cancelas, J. Zheng, D. A. Williams, Y. Zheng posted to drugdesign rac ras usa by allmensch on 2009-06-26 16:13:03 as along with 1 person chgjb
	Structure-based drug design: From nucleic acid to membrane protein targets [My Copy] Experimental and Molecular Pathology, Vol. 86, No. 3. (June 2009), pp. 141-150. by Magdalena M. Dailey, Chayanendu Hait, Patrick A. Holt, et al.Jon M. Maguire, Jason B. Meier, Clarke M. Miller, Luigi Petraccone, John O. Trent posted to drugdesign ras usa by allmensch on 2009-06-26 15:56:07 as
	A combined ligand-based and target-based drug design approach for G-protein coupled receptors: application to salvinorin A, a selective kappa opioid receptor agonist. [My Copy] J Comput Aided Mol Des (29 September 2006) by Nidhi Singh, Gwénaël Chevé, David M. Ferguson, Christopher R. McCurdy posted to no-tag by allmensch on 2009-06-26 15:53:40 as along with 1 person BragilMassoud
	COMBINE analysis of the specificity of binding of Ras proteins to their effectors [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 67, No. 2. (2007), pp. 435-447. by Sanja Tomi&cacute;, Branimir Bertoscarona, Ting Wang, Rebecca C. Wade posted to ras usa by allmensch on 2009-06-26 15:51:50 as
	Long-Time Protein Folding Dynamics from Short-Time Molecular Dynamics Simulations [My Copy] Multiscale Modeling & Simulation, Vol. 5, No. 4. (2006), pp. 1214-1226. by John D. Chodera, William C. Swope, Jed W. Pitera, Ken A. Dill posted to remd usa by allmensch on 2009-06-17 17:58:15 as along with 2 people ucbcjbm Diego_Prada
	Langevin dynamics of peptides: the frictional dependence of isomerization rates of N-acetylalanyl-N'-methylamide. [My Copy] Biopolymers, Vol. 32, No. 5. (May 1992), pp. 523-535. by R. J. Loncharich, B. R. Brooks, R. W. Pastor posted to remd usa by allmensch on 2009-06-17 17:40:47 as along with 2 people Lombardo_7 pavanghatty
	Overcoming stability limitations in biomolecular dynamics. I. Combining force splitting via extrapolation with Langevin dynamics in LN [My Copy] The Journal of Chemical Physics, Vol. 109, No. 5. (1998), pp. 1617-1632. by Eric Barth, Tamar Schlick posted to md remd usa by allmensch on 2009-06-17 17:39:47 as
	Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures [My Copy] Journal of Computational Chemistry, Vol. 25, No. 2. (30 January 2004), pp. 265-284. by Michael Feig, Alexey Onufriev, Michael S. Lee, Wonpil Im, David A. Case, Charles L. Brooks posted to gb md usa by allmensch on 2009-06-17 15:19:08 as along with 4 people itolokh yxue stephenbond Lombardo_7
	Extension to the weighted histogram analysis method: combining umbrella sampling with free energy calculations [My Copy] Computer Physics Communications, Vol. 135, No. 1. (15 March 2001), pp. 40-57. by Marc Souaille, Benoît Roux posted to tmd usa wham by allmensch on 2009-06-17 13:08:55 as along with 1 person stephenbond
	Structure of the guanine-nucleotide-binding domain of the Ha-ras oncogene product p21 in the triphosphate conformation. [My Copy] Nature, Vol. 341, No. 6239. (21 September 1989), pp. 209-214. by E. F. Pai, W. Kabsch, U. Krengel, K. C. Holmes, J. John, A. Wittinghofer posted to ras usa by allmensch on 2009-06-16 18:13:48 as
	Recent advances in the study of nucleic acid flexibility by molecular dynamics [My Copy] Current Opinion in Structural Biology, Vol. In Press, Corrected Proof by Modesto Orozco, Agnes Noy, Alberto Pérez posted to no-tag by allmensch on 2009-06-16 11:49:28 as along with 4 people and 1 group Elena_Zubova sobolevnrm onufriev mazo baker-group
	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 folding forcefield by allmensch on 2009-06-16 11:34:29 as along with 3 people bmduggan pablocarb loison
	Mapping the Nucleotide and Isoform-Dependent Structural and Dynamical Features of Ras Proteins [My Copy] Structure, Vol. 16, No. 6. (11 June 2008), pp. 885-896. by Alemayehu A. Gorfe, Barry J. Grant, Andrew J. Mccammon posted to ras usa by allmensch on 2009-06-15 14:15:03 as along with 1 person and 2 groups barry Bioinformatics structural_bioinformatics
	Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece. [My Copy] Journal of molecular biology, Vol. 374, No. 3. (30 November 2007), pp. 806-816. by D. L. Ensign, P. M. Kasson, V. S. Pande posted to folding trpzip by allmensch on 2009-06-15 13:40:36 as along with 1 person doktornoe
	Predicting peptide structures in native proteins from physical simulations of fragments. [My Copy] PLoS computational biology, Vol. 5, No. 2. (February 2009) by V. A. Voelz, M. S. Shell, K. A. Dill posted to ras usa by allmensch on 2009-06-15 11:59:16 as
	A Test on Peptide Stability of AMBER Force Fields with Implicit Solvation [My Copy] J. Phys. Chem. B (10 May 2008) by Scott M. Shell, Ryan Ritterson, Ken A. Dill posted to forcefield ras usa by allmensch on 2009-06-15 11:58:08 as along with 2 people onufriev middledomain
	Guanosine triphosphatase stimulation of oncogenic Ras mutants [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 96, No. 12. (8 June 1999), pp. 7065-7070. by Mohammad R. Ahmadian, Tsaffrir Zor, Dorothee Vogt, et al.Wolfgang Kabsch, Zvi Selinger, Alfred Wittinghofer, Klaus Scheffzek posted to ras usa by allmensch on 2009-06-12 11:34:26 as
	Ab initio Study of the Interactions between CO<SUB><FONT SIZE='-1'>2</FONT></SUB> and N-Containing Organic Heterocycles [My Copy] ChemPhysChem, Vol. 10, No. 2. (2009), pp. 374-383. by Konstantinos D. Vogiatzis, Andreas Mavrandonakis, Wim Klopper, George E. Froudakis posted to no-tag by allmensch on 2009-06-02 14:06:00 as
	Hydration of nucleic bases in dilute aqueous solutions. Apparent molar adiabatic and isothermal compressibilities, apparent molar volumes and their temperature slopes at 25 degrees C. [My Copy] Biophysical chemistry, Vol. 29, No. 3. (April 1988), pp. 283-292. by V. A. Buckin posted to fluorobases by allmensch on 2009-06-01 13:47:19 as
	The hydration and solvent polarization effects of nucleotide bases [My Copy] Biophysical Chemistry, Vol. 51, No. 2-3. (August 1994), pp. 253-261. by J. Gao posted to fluorobases by allmensch on 2009-06-01 13:45:52 as
	The G x U wobble base pair. A fundamental building block of RNA structure crucial to RNA function in diverse biological systems. [My Copy] EMBO Rep, Vol. 1, No. 1. (July 2000), pp. 18-23. by G. Varani, W. H. McClain posted to no-tag by allmensch on 2009-06-01 12:48:59 as along with 2 people evaf eskay

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usa	218
fluorobases	115
ras	102
md	59
nmr	54
lysozyme	43
unfoldedproteins	28
proteinfolding	24
trpzip	24
xray	19
drugtarget	17
nmrorderparameters	14
folding	13
protprot	13
forcfield	11
lysozym	9
mutations	9
relaxation	9
clustering	8
crystalstructure	8
pmf	8
complex	7
thr35	7
xraystructure	7
cancer	6
replicaexchange	6
taxol	6
allostery	5
boundtosugar	5
drugdesign	5
flexiblemeccano	5
protein	5
remd	5
unfoldedproteinstates	5
costellosyndrome	4
forcefield	4
kinase	4
modelfreeapproach	4
startingstructuredependence	4
statisticalerror	4
umbrellasampling	4
wham	4
clusterqualitymeasure	3
dynamics	3
flexibility	3
rna	3
transitionstate	3
alzheimer	2
amyloidaggregation	2
dssp	2
energylandscape	2
entropy	2
gb	2
gnm	2
inhibitor	2
ired	2
long-rangeinteractions	2
method	2
normalmodes	2
posttranslmod	2
proteinaggregation	2
rac	2
ramachandran	2
review	2
samplingproblem	2
secondary	2
strcuture	2
structure	2
temperaturedependence	2
transientpockets	2
unbiased	2
unfolded	2
xrayscattering	2
adiposis	1
backbonetorsionangles	1
betapeptide	1
bindingsites	1
complexnetworks	1
desmond	1
dihedralangledistance	1
dipolarcoupling	1
docking	1
ed	1
elasticnetworkmodel	1
energycalc	1
explremd	1
ff99	1
fl	1
fret	1
glycerol	1
gtpbound	1
hybrid	1
hybridremd	1
ide	1
isothermaltitration	1
kclust	1
kinetics	1
loop	1
mbar	1
mmtsb	1
mode-couplingsmoluchowskidynamics	1
nativeproteinconformations	1
neutrondiffraction	1
noe	1
orderparams	1
parkinson	1
pdb	1
pme	1
prion	1
proteindesign	1
proteinfoldingprobability	1
proteinpacking	1
ral	1
random-coilstatistics	1
rates	1
resp	1
rotamers	1
smc	1
sos	1
stabilitycurve	1
theory	1
thermostat	1
tip3p	1
tjump	1
tmd	1
torsionangles	1
trp-cage	1
xry	1

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