anuragsethi's library 65 articles Export

	Docking Flexible Peptide to Flexible Protein by Molecular Dynamics Using Two Implicit-Solvent Models: An Evaluation in Protein Kinase and Phosphatase Systems [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 43. (29 October 2009), pp. 14343-14354. by Zunnan Huang, Chung F. Wong posted to protein ligandbinding ligand_binding dynamics docking conformational_flexibility complexformation by anuragsethi on 2009-11-22 05:15:48 as along with 1 person and 1 group jmccammon McCammon
	Simulations of RNA Interactions with Monovalent Ions [My Copy] Methods in Enzymology, Vol. 469 (Nov 2009), pp. 411-432. by Alan A. Chen, M. Marucho, Nathan A. Baker, R. V. Pappu posted to rna ions dynamics by anuragsethi on 2009-11-19 22:47:30 as along with 1 person sobolevnrm
	Computational Identification of Slow Conformational Fluctuations in Proteins [My Copy] by Arvind Ramanathan, Pratul K. Agarwal posted to energyflow dynamics conformational_flexibility allostery by anuragsethi on 2009-11-16 22:19:04 as along with 1 person sobolevnrm
	Long-range energy transfer in proteins [My Copy] Physical Biology, Vol. 6 (Dec 2009) by Francesco Piazza, Yves H. Sanejouand posted to network enm energyflow coarse_grain allostery by anuragsethi on 2009-11-16 22:16:26 as along with 1 person sobolevnrm
	Multiscale characterization of protein conformational ensembles [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 76, No. 4. (2009), pp. 837-851. by Amarda Shehu, Lydia E. Kavraki, Cecilia Clementi posted to sampling_method multiscale energylandscape dynamics conformational_flexibility by anuragsethi on 2009-11-13 03:53:14 as along with 4 people and 3 groups okapi barry sobolevnrm apaydin structural_bioinformatics McCammon baker-group
	From the Cover: Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations [My Copy] Proc Natl Acad Sci USA, Vol. 106, No. 45. (Nov 2009), pp. 19011-19016. by F. Noé, C. Schütte, E. Vanden Eijnden, L. Reich, T. Weikl posted to sampling_method protein markov_models freeenergy folding energylandscape dynamics conformational_flexibility by anuragsethi on 2009-11-12 23:18:41 as along with 1 person sobolevnrm
	Conservation of Side-Chain Dynamics Within a Protein Family [My Copy] Journal of the American Chemical Society, Vol. 0, No. 0. (0000) by Anthony B. Law, Ernesto J. Fuentes, Andrew L. Lee posted to evolution dynamics conformational_flexibility by anuragsethi on 2009-11-10 19:22:34 as along with 4 people and 3 groups skywalkerus02 pablocarb barry sobolevnrm structural_bioinformatics McCammon baker-group
	Full correlation analysis of conformational protein dynamics [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA. by Oliver F. Lange, Helmut Grubmüller posted to dynamics correlation conformational_flexibility by anuragsethi on 2009-11-10 17:15:47 as along with 7 people and 1 group jeargle Diego_Prada softsimu barry choonpeng sobolevnrm LamBras baker-group
	Multi-scale characterization of the energy landscape of proteins with application to the C3D/Efb-C complex [My Copy] Proteins by Nurit Haspel, Brian V. Geisbrecht, John Lambris, Lydia Kavraki posted to sampling_method multiscale energylandscape dynamics conformational_flexibility complexformation by anuragsethi on 2009-11-10 17:13:34 as along with 1 person sobolevnrm
	Dynamical networks in tRNA:protein complexes [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 16. (21 April 2009), pp. 6620-6625. by Anurag Sethi, John Eargle, Alexis A. Black, Zaida Luthey-Schulten posted to rna protein network allostery by anuragsethi on 2009-11-09 04:25:50 as along with 4 people and 2 groups jeargle AbnerCYH jmccammon sobolevnrm McCammon baker-group
	Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms. [My Copy] Molecular bioSystems, Vol. 5, No. 3. (March 2009), pp. 207-216. by C. J. Tsai, A. Del Sol, R. Nussinov posted to network energyflow dynamics conformational_flexibility allostery by anuragsethi on 2009-11-07 16:33:25 as along with 4 people and 3 groups flbarroso barry sobolevnrm higueruelo structural_bioinformatics McCammon baker-group
	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 systemsbiology protein markov_models langevin complexformation by anuragsethi on 2009-11-07 16:32:41 as along with 3 people and 2 groups barry sobolevnrm jmccammon baker-group McCammon
	Allosteric Communication Occurs via Networks of Tertiary and Quaternary Motions in Proteins [My Copy] PLoS Comput Biol, Vol. 5, No. 2. (20 February 2009), e1000293. by Michael D. Daily, Jeffrey J. Gray posted to network allostery by anuragsethi on 2009-11-07 16:30:43 as along with 9 people and 3 groups skywalkerus02 sobolevnrm pablocarb AngelB eallain allmensch gane5h apaydin barry baker-group structural_bioinformatics McCammon
	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 kinase function freeenergy energylandscape conformational_flexibility allostery by anuragsethi on 2009-11-07 16:30:16 as along with 7 people and 2 groups Diego_Prada bmduggan allmensch guhjy sobolevnrm barry jmccammon baker-group McCammon
	Accelerating molecular dynamic simulation on graphics processing units [My Copy] Journal of Computational Chemistry, Vol. 30, No. 6. (2009), pp. 864-872. by Mark S. Friedrichs, Peter Eastman, Vishal Vaidyanathan, et al.Mike Houston, Scott Legrand, Adam L. Beberg, Daniel L. Ensign, Christopher M. Bruns, Vijay S. Pande posted to gpu dynamics by anuragsethi on 2009-11-07 16:29:52 as along with 10 people and 3 groups kevinchannon flbarroso r2s2 iantunbridge ihaque sobolevnrm ruvido massivemayhem barry RamuAnandakrishnan baker-group structural_bioinformatics McCammon
	Protein Dynamism and Evolvability [My Copy] Science, Vol. 324, No. 5924. (10 April 2009), pp. 203-207. by Nobuhiko Tokuriki, Dan S. Tawfik posted to function evolution dynamics conformational_flexibility by anuragsethi on 2009-11-07 16:29:11 as along with 19 people and 3 groups tomhebbron ahmetbakan kevinchannon klexa lauresultan dbikard ibuch ramiro2k barry pablocarb ramanuja sobolevnrm biomcgary hsekiguc VGreiff phoenixzxl zwang jdoconnell paulschlesinger structural_bioinformatics McCammon baker-group
	Computations of Standard Binding Free Energies with Molecular Dynamics Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 8. (26 February 2009), pp. 2234-2246. by Yuqing Deng, Benoît Roux posted to freeenergy energylandscape dynamics by anuragsethi on 2009-11-07 16:27:39 as along with 9 people and 2 groups flbarroso mikaellund sobolevnrm barry jmccammon willard agrossfield carlosjavierna ibuch baker-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 systemsbiology protein kinetics kinase complexformation by anuragsethi on 2009-11-07 16:26:48 as along with 10 people and 2 groups barry sunhwan jmccammon sobolevnrm willard kafuitay carlosjavierna sschurer hadesnumb paulschlesinger McCammon baker-group
	Similarity Measures for Protein Ensembles [My Copy] PLoS ONE, Vol. 4, No. 1. (15 January 2009), e4203. by Kresten Lindorff-Larsen, Jesper Ferkinghoff-Borg posted to pca energylandscape dynamics conformational_flexibility by anuragsethi on 2009-11-07 16:25:41 as along with 8 people and 3 groups klexa apaydin sobolevnrm gane5h barry jmccammon reyez biehl baker-group structural_bioinformatics McCammon
	Predicting pKa [My Copy] J. Chem. Inf. Model., Vol. 49, No. 9. (Sep 2009), pp. 2013-2033. by Adam C. Lee, Gordon M. Crippen posted to pka dynamics by anuragsethi on 2009-11-07 00:04:40 as along with 1 person sobolevnrm
	Analysis of relative influence of nodes in directed networks [My Copy] Phys. Rev. E, Vol. 80, No. 4. (Oct 2009) by Naoki Masuda, Yoji Kawamura, Hiroshi Kori posted to network by anuragsethi on 2009-11-02 19:20:48 as along with 1 person sobolevnrm
	Breaking the Curse of Dimensionality, Or How to Use SVD in Many Dimensions [My Copy] SIAM Journal on Scientific Computing, Vol. 31, No. 5. (Jan 2009), pp. 3744-3759. by I. V. Oseledets, E. E. Tyrtyshnikov posted to review pca by anuragsethi on 2009-11-02 19:19:58 as along with 1 person sobolevnrm
	Understanding protein structure from a percolation perspective [My Copy] Biophysical Journal, Vol. 97, No. 6. (Sep 2009), pp. 1787-94. by Dhruba Deb, Saraswathi Vishveshwara, Smitha Vishveshwara posted to protein percolation network by anuragsethi on 2009-11-02 17:45:40 as along with 1 person sobolevnrm
	Free Energy and Kinetics of Conformational Transitions from Voronoi Tessellated Milestoning with Restraining Potentials [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 10. (13 October 2009), pp. 2589-2594. by Luca Maragliano, Eric Vanden-Eijnden, Benoît Roux posted to network kinetics freeenergy free energylandscape conformational_flexibility by anuragsethi on 2009-10-31 04:32:06 as along with 1 person sobolevnrm
	A combinatorial approach to detect coevolved amino acid networks in protein families of variable divergence. [My Copy] PLoS computational biology, Vol. 5, No. 9. (4 September 2009), e1000488. by Julie Baussand, Alessandra Carbone posted to evolution coevolution bioinformatics by anuragsethi on 2009-10-31 04:29:08 as along with 6 people and 1 group dfdong sobolevnrm phoenixzxl maren barry zwang Bioinformatics
	Bend-twist-stretch model for coarse elastic network simulation of biomolecular motion [My Copy] The Journal of Chemical Physics, Vol. 131, No. 7. (2009), 074112. by Joseph N. Stember, Willy Wriggers posted to forcefield enm allostery by anuragsethi on 2009-10-27 17:13:11 as along with 2 people sobolevnrm agrossfield
	Bridging from molecular simulation to biochemical networks. [My Copy] Curr Opin Struct Biol, Vol. 17, No. 2. (April 2007), pp. 166-172. by M. Stein, R. R. Gabdoulline, R. C. Wade posted to systemsbiology dynamics brownian_dynamics by anuragsethi on 2009-10-25 16:33:47 as along with 9 people and 1 group choonpeng oteri ocs aqeel Borelli cmmorel julius ras higueruelo Structural Biology Group TorVergata
	Convergence of sampling in protein simulations [My Copy] Physical Review E, Vol. 65, No. 3. (1 March 2002), 031910. by Berk Hess posted to pca dynamics correlation convergence conformational_flexibility by anuragsethi on 2009-10-25 16:31:04 as along with 5 people and 1 group klexa tovrstra oteri onufriev softsimu Structural Biology Group TorVergata
	Chapter 4 Accelerated Molecular Dynamics Methods: Introduction and Recent Developments [My Copy] In Annual Reports in Computational Chemistry Volume 5, Vol. 5 (2009), pp. 79-98. by Danny Perez, Blas P. Uberuaga, Yunsic Shim, Jacques G. Amar, Arthur F. Voter posted to replica dynamics accelerated by anuragsethi on 2009-10-25 16:29:18 as along with 1 person and 1 group oteri Structural Biology Group TorVergata
	The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations. [My Copy] Journal of Physical Chemistry B, Vol. 111, No. 27. (1 July 2007), pp. 7812-7824. by Siewert J. Marrink, H. J. Risselada, Serge Yefimov, D. P. Tieleman, Alex H. Vries posted to forcefield coarse_grain by anuragsethi on 2009-10-25 03:00:52 as along with 7 people and 2 groups sunrise A_Coletta_Thesis Marine choonpeng softsimu dimka sunnytov Structural Biology Group TorVergata Molecular dynamics in MSU
	Novel Families of Putative Protein Kinases in Bacteria and Archaea: Evolution of the âEukaryoticâ Protein Kinase Superfamily [My Copy] Genome Research, Vol. 8, No. 10. (1 October 1998), pp. 1038-1047. by Christopher J. Leonard, L. Aravind, Eugene V. Koonin posted to kinase evolution bioinformatics bacteria archaea by anuragsethi on 2009-10-23 07:20:58 as along with 3 people and 1 group robfsouza thegoose2 tharris C. elegans / WormBase
	Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms [My Copy] Journal of Chemical Theory and Computation, Vol. 3, No. 6. (1 November 2007), pp. 2312-2334. by Jianyin Shao, Stephen W. Tanner, Nephi Thompson, Thomas E. Cheatham posted to dynamics clustering allostery by anuragsethi on 2009-10-23 07:19:08 as along with 9 people and 3 groups Diego_Prada scampos oteri barry daevans sobolevnrm LamBras allmensch GermanErlenkamp Structural Biology Group TorVergata structural_bioinformatics baker-group
	Discovery Through the Computational Microscope [My Copy] Vol. 17, No. 10. (14 October 2009), pp. 1295-1306. by Eric H. Lee, Jen Hsin, Marcos Sotomayor, Gemma Comellas, Klaus Schulten posted to review dynamics by anuragsethi on 2009-10-23 07:16:18 as along with 1 person agrossfield
	Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: The myoglobin case [My Copy] Journal of Molecular Graphics and Modelling, Vol. 27, No. 8. (June 2009), pp. 889-899. by Elena Papaleo, Paolo Mereghetti, Piercarlo Fantucci, Rita Grandori, Luca De Gioia posted to pca energylandscape energyflow dynamics correlation conformational_flexibility clustering allostery by anuragsethi on 2009-10-23 07:15:44 as along with 1 person dimka
	How To Choose a Good Scientific Problem [My Copy] Molecular Cell, Vol. 35, No. 6. (24 September 2009), pp. 726-728. by Uri Alon posted to scientist science by anuragsethi on 2009-10-22 03:00:38 as along with 124 people and 6 groups artaban421 cefa gvdh penneyft welliegirl bertelsen thegoose xawen chriswillmott nellapower ishiken andreff claudiushauptmann cermak bmoores karthikraman applebyb mordiano Gorzomagnificent Horduna ajaymalik mmwoodman dbikard toszko mthomure timflutre cyounkin marsl0am jmzhuo dmorti renatomilani ibre kevinemamy Sergey_gerbek huberse ddbb12 seneca mattbiehl mmborges GeeSharpMinor jjjpppfff zhangfh andreacapocci melo_mcr aaltenburger iannis jichok josephjose TorstenWaldminghaus kshameer rudalert kvalyi duel_jetty allaves rabit fercosber hax123 iskanbasal livingthingdan poojamaj gonzalez amynmoore ramalldf pvdg sfalsharif dill2009 singhsh rogermug aha jarekadam Jansen04 cgravlee lkakinami flips robfree kaliczp yyfwuhan luciensamary elsantosneto mgaldino daveGerrard sandfire tnhh lesandrop munzmarci pdpcosta mxro wangngu myriasofo OliverHarriman AnthonySoprano robertlischke R_C_Cordeiro daforerog operon nandipati wenhaosparty jeffcrow leocmcheung fgibson snakehsu cisevol michaelbarton dna dullhunk danilov m_lew abellogin cxshang grahamc SantoshKalwar Xusheng leonardo roys benoitvalley zchen75 darshan druvus Asclepius Zephyrus songpku aalibes flieder pedromts Brain-like research group UWA Science Communication milab@yzu Information Integration Architecture BergmanLab Roswell Cancer Crosstalk
	Computation of conformational transitions in proteins by virtual atom molecular mechanics as validated in application to adenylate kinase [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 37. (15 September 2009), pp. 15673-15678. by Anil Korkut, Wayne A. Hendrickson posted to enm dynamics conformational_flexibility by anuragsethi on 2009-10-18 20:53:11 as along with 1 person and 1 group jmccammon McCammon
	Multiscale simulation of soft matter systems - from the atomistic to the coarse-grained level and back [My Copy] Soft Matter, Vol. 5, No. 22. (2009), pp. 4357-4366. by Christine Peter, Kurt Kremer posted to review forcefield dynamics coarse_grain by anuragsethi on 2009-10-17 14:15:45 as along with 2 people flbarroso sobolevnrm
	Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 9. (8 September 2009), pp. 2486-2502. by Christopher L. McClendon, Gregory Friedland, David L. Mobley, Homeira Amirkhani, Matthew P. Jacobson posted to dynamics biology allostery by anuragsethi on 2009-10-17 14:13:25 as along with 3 people and 1 group jmccammon pmung acpan McCammon
	Community evolution in dynamic multi-mode networks [My Copy] In KDD '08: Proceeding of the 14th ACM SIGKDD international conference on Knowledge discovery and data mining (2008), pp. 677-685. by Lei Tang, Huan Liu, Jianping Zhang, Zohreh Nazeri posted to network mathematics evolution dynamics community by anuragsethi on 2009-10-17 14:10:31 as along with 1 person rocling
	Protein elastic network models and the ranges of cooperativity [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 30. (28 July 2009), pp. 12347-12352. by Lei Yang, Guang Song, Robert L. Jernigan posted to network enm dynamics conformational_flexibility allostery by anuragsethi on 2009-10-16 17:23:01 as along with 4 people Diego_Prada sobolevnrm apaydin edws
	Enzymatic Activity versus Structural Dynamics: The Case of Acetylcholinesterase Tetramer [My Copy] Vol. 97, No. 3. (5 August 2009), pp. 897-905. by Alemayehu A. Gorfe, Benzhuo Lu, Zeyun Yu, J. Andrew McCammon posted to function dynamics by anuragsethi on 2009-10-16 02:28:10 as along with 1 person sobolevnrm
	Atomistic View of the Conformational Activation of Src Kinase Using the String Method with Swarms-of-Trajectories [My Copy] Biophysical Journal, Vol. 97, No. 4. (19 August 2009), pp. L8-L10. by Wenxun Gan, Sichun Yang, Benoît Roux posted to freeenergy energylandscape allostery by anuragsethi on 2009-10-16 02:26:57 as along with 1 person and 1 group jmccammon McCammon
	The Origin of Allosteric Functional Modulation: Multiple Pre-existing Pathways [My Copy] Vol. 17, No. 8. (12 August 2009), pp. 1042-1050. by Antonio del Sol, Chung-Jung Tsai, Buyong Ma, Ruth Nussinov posted to energylandscape energyflow allostery by anuragsethi on 2009-10-16 02:25:36 as along with 1 person sobolevnrm
	Systematic coarse graining from structure using internal states: Application to phospholipid/cholesterol bilayer [My Copy] The Journal of Chemical Physics, Vol. 131, No. 5. (2009), 055101. by Teemu Murtola, Mikko Karttunen, Ilpo Vattulainen posted to dynamics coarse_grain by anuragsethi on 2009-10-07 14:27:07 as along with 3 people sobolevnrm cjryan agrossfield
	Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint [My Copy] The Journal of Chemical Physics, Vol. 131, No. 4. (2009), 045106. by Sergio Bacallado, John D. Chodera, Vijay Pande posted to markov_models freeenergy energylandscape dynamics by anuragsethi on 2009-10-05 14:38:43 as along with 3 people and 1 group sobolevnrm whitead dlimmer Jiang Research Group
	Know your limits: Assumptions, constraints and interpretation in systems biology [My Copy] Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics, Vol. 1794, No. 9. (09 September 2009), pp. 1280-1287. by Garth R. Ilsley, Nicholas M. Luscombe, Rolf Apweiler posted to systemsbiology review by anuragsethi on 2009-09-28 00:39:22 as along with 1 person sobolevnrm
	Analysing the origin of long-range interactions in proteins using lattice models [My Copy] BMC Structural Biology, Vol. 9, No. 1. (29 January 2009), 4. by Orly N. Brik, Ron Unger, Amnon Horovitz posted to lattice_models dynamics allostery by anuragsethi on 2009-09-28 00:37:39 as along with 2 people and 2 groups barry sobolevnrm structural_bioinformatics McCammon
	The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 34. (25 August 2009), pp. 14349-14354. by Ahmet Bakan, Ivet Bahar posted to network ligand_binding dynamics conformational_flexibility by anuragsethi on 2009-09-16 14:26:38 as along with 5 people and 1 group ahmetbakan apaydin jmccammon okapi boris_aguilar McCammon
	RedMD - Reduced molecular dynamics package [My Copy] Journal of Computational Chemistry, Vol. 30, No. 14. (2009), pp. 2364-2373. by Adam Górecki, Marcin Szypowski, Maciej D&lstrok;ugosz, Joanna Trylska posted to multiscale dynamics brownian_dynamics by anuragsethi on 2009-09-16 14:23:36 as along with 4 people and 1 group oteri flbarroso jmccammon shwu McCammon
	Conformational selection or induced fit: A flux description of reaction mechanism [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 33. (18 August 2009), pp. 13737-13741. by Gordon G. Hammes, Yu-Chu Chang, Terrence G. Oas posted to ligandbinding freeenergy complexformation allostery by anuragsethi on 2009-09-13 05:13:28 as along with 4 people and 1 group chemrahul82 xdeupi pmung barry McCammon

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dynamics	39
allostery	18
conformational_flexibility	17
network	14
energylandscape	13
freeenergy	10
protein	9
complexformation	6
energyflow	6
evolution	6
function	5
bioinformatics	4
coarse_grain	4
enm	4
forcefield	4
ligandbinding	4
multiscale	4
pca	4
review	4
systemsbiology	4
correlation	3
kinase	3
markov_models	3
sampling_method	3
biology	2
brownian_dynamics	2
clustering	2
community	2
ions	2
kinetics	2
ligand_binding	2
mathematics	2
pka	2
rna	2
accelerated	1
alignment	1
archaea	1
bacteria	1
coevolution	1
convergence	1
docking	1
entropy	1
folding	1
free	1
gpu	1
langevin	1
lattice_models	1
nucleic	1
percolation	1
replica	1
ribosome	1
science	1
scientist	1
structure	1
systems	1
timedelay	1
translation	1
water	1

anuragsethi's library 65 articles Export

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