ttjoseph's library 84 articles Export

	Protein simulation below the glass-transition temperature. Dependence on cooling protocol [My Copy] Chemical Physics Letters, Vol. 226, No. 5-6. (26 August 1994), pp. 447-452. by Peter J. Steinbach, Bernard R. Brooks posted to molecular-dynamics simulated-annealing by ttjoseph on 2007-03-07 18:29:06 as
	All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins† [My Copy] The Journal of Physical Chemistry B, Vol. 102, No. 18. (1 April 1998), pp. 3586-3616. by A. D. MacKerell, D. Bashford, Bellott, et al.R. L. Dunbrack, J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, M. Karplus posted to force-field molecular-dynamics by ttjoseph on 2007-03-07 04:39:41 as along with 12 people jmparks dsmueller rpetrenko jrperillaj Diego_Prada oceanwind dfgreen mkrishna timg dimka papatonyhill ssomani
	Automated docking of flexible ligands: Applications of autodock [My Copy] Journal of Molecular Recognition, Vol. 9, No. 1. (1996), pp. 1-5. by David S. Goodsell, Garrett M. Morris, Arthur J. Olson posted to docking by ttjoseph on 2007-03-07 04:35:10 as
	New-Generation Amber United-Atom Force Field [My Copy] J. Phys. Chem. B, Vol. 110, No. 26. (6 July 2006), pp. 13166-13176. by L. Yang, C. Tan, M. J. Hsieh, et al.J. Wang, Y. Duan, P. Cieplak, J. Caldwell, P. A. Kollman, R. Luo posted to force-field molecular-dynamics by ttjoseph on 2007-03-07 04:34:09 as along with 1 person krapnik
	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 force-field molecular-dynamics by ttjoseph on 2007-03-07 04:08:15 as along with 17 people and 1 group jmparks fralium bmduggan kulinskii ibuch Lombardo_7 paddydu dfgreen softsimu mleis ffranca easybakemuffin ashaytan RamuAnandakrishnan r2s2 pavanghatty Diego_Prada CMB
	Crystal Structures of RNase H Bound to an RNA/DNA Hybrid: Substrate Specificity and Metal-Dependent Catalysis [My Copy] Cell, Vol. 121, No. 7. (1 July 2005), pp. 1005-1016. by Marcin Nowotny, Sergei A. Gaidamakov, Robert J. Crouch, Wei Yang posted to cleavage crystal-structure rnase-h by ttjoseph on 2007-03-07 04:05:10 as
	Steered molecular dynamics and mechanical functions of proteins [My Copy] Current Opinion in Structural Biology, Vol. 11, No. 2. (1 April 2001), pp. 224-230. by B. Isralewitz posted to molecular-dynamics by ttjoseph on 2007-03-06 02:37:04 as along with 4 people and 2 groups Diego_Prada devinli barry LamBras structural_bioinformatics Bioinformatics
	Simulated annealing with restrained molecular dynamics using a flexible restraint potential: Theory and evaluation with simulated NMR constraints [My Copy] Protein Sci, Vol. 5, No. 4. (1 April 1996), pp. 593-603. by D. Bassolino-Klimas, R. Tejero, S. R. Krystek, W. J. Metzler, G. T. Montelione, R. E. Bruccoleri posted to molecular-dynamics simulated-annealing by ttjoseph on 2007-03-06 01:36:22 as along with 1 person laurabailey
	Scalable molecular dynamics with NAMD [My Copy] Journal of Computational Chemistry, Vol. 26, No. 16. (December 2005), pp. 1781-1802. by James C. Phillips, Rosemary Braun, Wei Wang, et al.James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kalé, Klaus Schulten posted to molecular-dynamics software by ttjoseph on 2007-03-02 16:13:33 as along with 20 people and 5 groups krapnik pjkiley flbarroso yxue r2s2 grondina rpetrenko oteri oceanwind dfgreen vahmurk gisle dimka jwm sangeetha yoel_rf bilab wilsoros sobolevnrm ibuch Radiation_Damage Stressosome Bioinformatics insilicodrug baker-group
	Multi-Terminal Network Flows [My Copy] Journal of the Society for Industrial and Applied Mathematics, Vol. 9, No. 4. (1961), pp. 551-570. by R. E. Gomory, T. C. Hu posted to cs graph-theory by ttjoseph on 2007-03-02 03:33:12 as
	Coarse-Graining in Polymer Simulation: From the Atomistic to the Mesoscopic Scale and Back [My Copy] ChemPhysChem, Vol. 3, No. 9. (2002), pp. 754-769. by Florian Müller-Plathe posted to coarse-graining simulation by ttjoseph on 2007-02-28 22:55:38 as along with 2 people sunrise kaz229
	Graph Clustering and Minimum Cut Trees [My Copy] Internet Mathematics, Vol. 1, No. 4. (2004), pp. 385-408. by Gary W. Flake, Robert E. Tarjan, Kostas Tsioutsiouliklis posted to cs graph-theory by ttjoseph on 2007-02-22 02:11:06 as along with 2 people rocarvaj AbnerCYH
	Structure of the C-terminal half of UvrC reveals an RNase H endonuclease domain with an Argonaute-like catalytic triad. [My Copy] EMBO J, Vol. 26, No. 2. (24 January 2007), pp. 613-622. by E. Karakas, J. J. Truglio, D. Croteau, et al.B. Rhau, L. Wang, B. Van Houten, C. Kisker posted to argonaute by ttjoseph on 2007-01-30 00:49:06 as
	Comparison of siRNA-induced off-target RNA and protein effects [My Copy] RNA, Vol. 13, No. 3. (19 March 2007), pp. 385-395. by Lourdes M. AlemÃ¡n, John Doench, Phillip A. Sharp posted to sirna rnai by ttjoseph on 2007-01-30 00:48:38 as along with 1 person heliopais
	Can Principal Components Yield a Dimension Reduced Description of Protein Dynamics on Long Time Scales? [My Copy] J. Phys. Chem. B, Vol. 110, No. 45. (16 November 2006), pp. 22842-22852. by O. F. Lange, H. Grubmuller posted to molecular-dynamics essential-dynamics biophysics by ttjoseph on 2007-01-18 16:44:01 as along with 1 person ffranca
	Stitching together RNA tertiary architectures [My Copy] Journal of Molecular Biology, Vol. 294, No. 4. (10 December 1999), pp. 829-849. by Thomas Hermann, Dinshaw J. Patel posted to rna structure by ttjoseph on 2006-11-29 22:03:29 as along with 3 people and 3 groups marcius condon jarasch beta BioinfoCIPF SGU-CIPF
	Widespread siRNA "off-target" transcript silencing mediated by seed region sequence complementarity. [My Copy] RNA (8 May 2006) by Aimee L L. Jackson, Julja Burchard, Janell Schelter, et al.B Nelson N. Chau, Michele Cleary, Lee Lim, Peter S S. Linsley posted to rnai by ttjoseph on 2006-11-23 05:07:55 as along with 4 people diaz0058 tardigrade lhonigberg mtagaya
	Structural domains in RNAi. [My Copy] FEBS Lett, Vol. 579, No. 26. (31 October 2005), pp. 5841-5849. by R. E. Collins, X. Cheng posted to rnai by ttjoseph on 2006-11-08 21:22:35 as
	Therapeutic RNA interference of malignant melanoma by electrotransfer of small interfering RNA targeting Mitf [My Copy] Gene Therapy, Vol. aop, No. current. by N. Nakai, T. Kishida, M. Shin-Ya, et al.J. Imanishi, Y. Ueda, S. Kishimoto, O. Mazda, posted to rnai therapeutics by ttjoseph on 2006-11-01 20:31:08 as
	Control of translation and mRNA degradation by miRNAs and siRNAs. [My Copy] Genes Dev, Vol. 20, No. 5. (1 March 2006), pp. 515-524. by M. A. Valencia-Sanchez, J. Liu, G. J. Hannon, R. Parker posted to argonaute rnai by ttjoseph on 2006-10-30 04:56:49 as along with 3 people perrywoo osman bertelsen
	Argonaute: a scaffold for the function of short regulatory RNAs. [My Copy] Trends Biochem Sci (5 October 2006) by James S S. Parker, David Barford posted to argonaute rnai by ttjoseph on 2006-10-29 00:11:33 as along with 3 people and 2 groups micromassive dchughes mtagaya G4ID Genetics-of-Gambling
	Argonaute-1 directs siRNA-mediated transcriptional gene silencing in human cells. [My Copy] Nat Struct Mol Biol (27 August 2006) by Daniel H H. Kim, Louisa M M. Villeneuve, Kevin V V. Morris, John J J. Rossi posted to argonaute rnai by ttjoseph on 2006-10-29 00:11:13 as along with 4 people tardigrade mtagaya elzodw sebastien_vigneau
	Contributions of 3'-overhang to the dissociation of small interfering RNAs from the PAZ domain: Molecular dynamics simulation study. [My Copy] J Mol Graph Model (11 July 2006) by Hui Sun S. Lee, Soo Nam N. Lee, Chul Hyun H. Joo, et al.Heuiran Lee, Han Saem S. Lee, Seung Yong Y. Yoon, Yoo Kyum K. Kim, Han Choe posted to molecular-dynamics rnai sirna by ttjoseph on 2006-10-12 01:47:11 as along with 1 person tardigrade
	How do substrates enter and products exit the buried active site of cytochrome P450cam? 1. Random expulsion molecular dynamics investigation of ligand access channels and mechanisms [My Copy] Journal of Molecular Biology, Vol. 303, No. 5. (10 November 2000), pp. 797-811. by Susanna K. Ludemann, Valere Lounnas, Rebecca C. Wade posted to molecular-dynamics remd by ttjoseph on 2006-10-10 23:00:00 as
	From the Cover: Free energy reconstruction from nonequilibrium single-molecule pulling experiments [My Copy] PNAS, Vol. 98, No. 7. (27 March 2001), pp. 3658-3661. by Gerhard Hummer, Attila Szabo posted to biophysics free-energy molecular-dynamics by ttjoseph on 2006-09-29 16:03:20 as along with 4 people and 1 group cjryan cgguido dchen onufriev WeeksLab
	Thermodynamic calculations in biological systems [My Copy] Biophysical Chemistry, Vol. In Press, Corrected Proof by Mario L. Amzel, Xavier Siebert, Anthony Armstrong, German Pabon posted to biophysics molecular-dynamics by ttjoseph on 2006-09-29 15:59:20 as along with 6 people and 3 groups Scis0000002 barry pansapiens shuns imouthesmp nknii structural_bioinformatics Bioinformatics TCR_Signaling
	Structural dynamics of precursor and product of the RNA enzyme from the hepatitis delta virus as revealed by molecular dynamics simulations. [My Copy] J Mol Biol, Vol. 351, No. 4. (26 August 2005), pp. 731-748. by M. V. Krasovska, J. Sefcikova, N. Spacková, J. Sponer, N. G. Walter posted to cleavage molecular-dynamics by ttjoseph on 2006-09-29 03:38:01 as
	Kinetics from Nonequilibrium Single-Molecule Pulling Experiments [My Copy] Biophys. J., Vol. 85, No. 1. (1 July 2003), pp. 5-15. by Gerhard Hummer, Attila Szabo posted to biophysics by ttjoseph on 2006-09-29 02:40:39 as
	Calculation of absolute protein-ligand binding free energy from computer simulations. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 19. (10 May 2005), pp. 6825-6830. by H. J. Woo, B. Roux posted to free-energy molecular-dynamics by ttjoseph on 2006-09-29 00:39:35 as along with 4 people flbarroso ibuch LamBras ashaytan
	Model-free methods of analyzing domain motions in proteins from simulation: a comparison of normal mode analysis and molecular dynamics simulation of lysozyme. [My Copy] Proteins, Vol. 27, No. 3. (March 1997), pp. 425-437. by S. Hayward, A. Kitao, H. J. Berendsen posted to biophysics collective-dynamics essential-dynamics molecular-dynamics by ttjoseph on 2006-08-18 06:31:09 as along with 1 person Scis0000002
	On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations [My Copy] Proteins: Structure, Function, and Genetics, Vol. 36, No. 4. (1999), pp. 419-424. by Andrea Amadei, Marc A. Ceruso, Alfredo Di Nola posted to essential-dynamics molecular-dynamics by ttjoseph on 2006-08-07 18:35:39 as along with 1 person scampos
	Molecular dynamics simulations of biomolecules: long-range electrostatic effects. [My Copy] Annu Rev Biophys Biomol Struct, Vol. 28 (1999), pp. 155-179. by C. Sagui, T. A. Darden posted to electrostatics molecular-dynamics particle-mesh-ewald by ttjoseph on 2006-04-28 21:25:24 as along with 8 people Scis0000002 babakap onufriev lillekatt dgront RamuAnandakrishnan AndreaColetta r2s2
	Argonaute and RNA--getting into the groove. [My Copy] Curr Opin Struct Biol, Vol. 16, No. 1. (February 2006), pp. 5-11. by J. J. Song, L. Joshua-Tor posted to argonaute rnai by ttjoseph on 2006-04-06 01:44:40 as
	Exploring the Helix-Coil Transition via All-Atom Equilibrium Ensemble Simulations. [My Copy] Biophys J, Vol. 88, No. 4. (April 2005), pp. 2472-2493. by E. J. Sorin, V. S. Pande posted to biophysics force-field molecular-dynamics by ttjoseph on 2006-04-03 15:34:45 as along with 3 people krapnik allmensch loison
	A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules [My Copy] Journal of the American Chemical Society, Vol. 117, No. 19. (1995), pp. 5179-5197. by Wendy D. Cornell, Piotr Cieplak, Christopher I. Bayly, et al.Ian R. Gould, Kenneth M. Merz, David M. Ferguson, David C. Spellmeyer, Thomas Fox, James W. Caldwell, Peter A. Kollman posted to biophysics force-field by ttjoseph on 2006-04-03 15:33:09 as
	Steered molecular dynamics [My Copy] In Computational Molecular Dynamics: Challenges, Methods, Ideas, Vol. 4 (1998), pp. 39-65. by S. Izrailev, S. Stepaniants, B. Isralewitz, et al.D. Kosztin, H. Lu, F. Molnar, W. Wriggers, K. Schulten edited by P. Deuflhard, J. Hermans, B. Leimkuhler, A. E. Mark, S. Reich, R. D. Skeel posted to molecular-dynamics by ttjoseph on 2006-04-01 04:54:39 as
	A heuristic procedure for the detection of locally similar substructures of two equivalent structures. [My Copy] Protein Eng, Vol. 7, No. 3. (March 1994), pp. 331-333. by M. Mezei posted to algorithms biophysics flexibility by ttjoseph on 2006-03-31 08:11:19 as along with 1 person dimka
	Crystal structure of a PIWI protein suggests mechanisms for siRNA recognition and slicer activity [My Copy] The EMBO Journal, Vol. aop, No. current. (02 December 2004) by James S. Parker, S. Mark Roe, David Barford posted to argonaute crystal-structure rnai by ttjoseph on 2006-03-31 06:09:13 as along with 1 person tardigrade
	Rapid protein-ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: binding of FK506 to FKBP. [My Copy] Proteins, Vol. 54, No. 4. (1 March 2004), pp. 759-767. by M. Zacharias posted to docking essential-dynamics molecular-dynamics by ttjoseph on 2006-03-30 21:15:49 as along with 2 people dgruiz RamuAnandakrishnan
	Comparative study of generalized Born models: protein dynamics. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 19. (10 May 2005), pp. 6760-6764. by H. Fan, A. E. Mark, J. Zhu, B. Honig posted to generalized-born gromacs by ttjoseph on 2006-03-13 05:22:58 as along with 1 person krapnik
	Rigid Protein Motion as a Model for Crystallographic Temperature Factors [My Copy] Proceedings of the National Academy of Sciences USA, Vol. 88 (April 1991), pp. 2773-2777. by John Kuriyan, William I. Weis posted to biophysics by ttjoseph on 2006-03-12 16:28:56 as
	A note on two problems in connexion with graphs [My Copy] Numerische Mathematik, Vol. 1, No. 1. (December 1959), pp. 269-271. by E. W. Dijkstra posted to algorithms graph-theory by ttjoseph on 2006-03-09 22:02:04 as along with 1 person cari
	Comparative protein structure modeling of genes and genomes. [My Copy] Annual review of biophysics and biomolecular structure, Vol. 29 (2000), pp. 291-325. by M. A. Martí-Renom, A. C. Stuart, A. Fiser, R. Sánchez, F. Melo, A. Sali posted to homology-modeling by ttjoseph on 2006-03-09 21:44:40 as along with 15 people and 2 groups tjimenez jperkins fautore aalibes nigham chad_davis marcius ffranca duartemolha dgront ruvido insectopalo min013 IrinaMoreira granujilla BioinfoCIPF SGU-CIPF
	Optimization by Simulated Annealing [My Copy] Science, Vol. 220, No. 4598. (1983), pp. 671-680. by S. Kirkpatrick, Gelatt Cd, Vecchi Mp posted to algorithms simulated-annealing by ttjoseph on 2006-02-27 03:01:42 as along with 14 people BragilMassoud filippone martinthesis mseise Bc91 ilapla markusd wvangeit andrewmercader fernandohbc slatre guxiyou pawelt dcastro
	Evidence that siRNAs function as guides, not primers, in the Drosophila and human RNAi pathways. [My Copy] Mol Cell, Vol. 10, No. 3. (September 2002), pp. 537-548. by D. S. Schwarz, G. Hutvágner, B. Haley, P. D. Zamore posted to rnai by ttjoseph on 2006-02-27 00:32:26 as
	Structure and conserved RNA binding of the PAZ domain. [My Copy] Nature, Vol. 426, No. 6965. (27 November 2003), pp. 468-474. by K. S. Yan, S. Yan, A. Farooq, A. Han, L. Zeng, M. M. Zhou posted to rnai by ttjoseph on 2006-02-27 00:23:52 as along with 1 person tardigrade
	Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain [My Copy] Nature, Vol. 429, No. 6989. (20 May 2004), pp. 318-322. by Jin-Biao Ma, Keqiong Ye, Dinshaw J. Patel posted to rnai by ttjoseph on 2006-02-26 02:01:04 as along with 1 person tardigrade
	Kinetic analysis of the RNAi enzyme complex. [My Copy] Nat Struct Mol Biol, Vol. 11, No. 7. (July 2004), pp. 599-606. by B. Haley, P. D. Zamore posted to rnai by ttjoseph on 2006-02-26 01:57:19 as
	Specificity of microRNA target selection in translational repression. [My Copy] Genes Dev, Vol. 18, No. 5. (1 March 2004), pp. 504-511. by J. G. Doench, P. A. Sharp posted to rnai by ttjoseph on 2006-02-26 01:56:42 as along with 4 people pengchy evaf tardigrade mtagaya
	'Protein Peeling': an approach for splitting a 3D protein structure into compact fragments [My Copy] Bioinformatics, Vol. 22, No. 2. (15 January 2006), pp. 129-133. by Jean-Christophe Gelly, Alexandre G. de Brevern, Serge Hazout posted to algorithms by ttjoseph on 2006-02-01 23:01:26 as along with 6 people and 4 groups ana barry dimka marcius nickolay choonpeng structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF

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rnai	27
molecular-dynamics	22
argonaute	15
biophysics	9
essential-dynamics	7
crystal-structure	6
algorithms	5
docking	5
force-field	5
generalized-born	5
sirna	4
graph-theory	3
simulated-annealing	3
software	3
statistics	3
cleavage	2
collective-dynamics	2
cs	2
flexibility	2
free-energy	2
gromacs	2
amber	1
coarse-graining	1
electrostatics	1
homology-modeling	1
mirna	1
modloop	1
monte-carlo	1
particle-mesh-ewald	1
piwi	1
poisson-boltzmann	1
remd	1
rna	1
rnase-h	1
simulation	1
structural-alignment	1
structure	1
therapeutics	1

ttjoseph's library 84 articles Export

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