okapi's library 40 articles Export

	Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 46. (17 November 2009), pp. 19346-19351. by Tomasz Wlodarski, Bojan Zagrovic posted to allostery by okapi on 2009-11-28 09:13:00 as along with 1 person ahmetbakan
	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 allostery by okapi on 2009-11-27 09:30:03 as along with 5 people and 1 group chemrahul82 xdeupi anuragsethi pmung barry McCammon
	Actin, a Central Player in Cell Shape and Movement [My Copy] Science, Vol. 326, No. 5957. (27 November 2009), pp. 1208-1212. by Thomas D. Pollard, John A. Cooper posted to motor by okapi on 2009-11-27 05:16:18 as along with 2 people flbarroso eango
	Membrane Binding by the Endophilin N-BAR Domain [My Copy] Vol. 97, No. 10. (15 November 2009), pp. 2746-2753. by Haosheng Cui, Gary S. Ayton, Gregory A. Voth posted to simulation membrane by okapi on 2009-11-26 10:21:04 as
	Membrane-Bending Mechanism of Amphiphysin N-BAR Domains [My Copy] Vol. 97, No. 10. (15 November 2009), pp. 2727-2735. by Anton Arkhipov, Ying Yin, Klaus Schulten posted to simulation membrane coarse-grain by okapi on 2009-11-26 10:16:46 as
	What recent ribosome structures have revealed about the mechanism of translation [My Copy] Nature, Vol. 461, No. 7268. (18 October 2009), pp. 1234-1242. by T. Martin Schmeing, V. Ramakrishnan posted to motor by okapi on 2009-11-25 07:50:15 as along with 6 people and 1 group caducadu Winzer dchughes ppgardne pedrobeltrao richardfranzese Journal picks
	Exploitation of binding energy for catalysis and design [My Copy] Nature, Vol. 461, No. 7268. (29 October 2009), pp. 1300-1304. by Summer B. Thyme, Jordan Jarjour, Ryo Takeuchi, et al.James J. Havranek, Justin Ashworth, Andrew M. Scharenberg, Barry L. Stoddard, David Baker posted to protein_design by okapi on 2009-11-23 12:09:31 as along with 3 people flbarroso pablocarb yse
	Mechanism of Robust Circadian Oscillation of KaiC Phosphorylation In Vitro [My Copy] Vol. 95, No. 4. (15 August 2008), pp. 1773-1784. by Kohei Eguchi, Mitsumasa Yoda, Tomoki P. Terada, Masaki Sasai posted to circadian_rhythm by okapi on 2009-11-20 07:56:10 as
	Monomer-Shuffling and Allosteric Transition in KaiC Circadian Oscillation [My Copy] PLoS ONE, Vol. 2, No. 5. (2007), e408. by Mitsumasa Yoda, Kohei Eguchi, Tomoki P. Terada, Masaki Sasai posted to circadian_rhythm by okapi on 2009-11-20 07:49:13 as
	Autonomous synchronization of the circadian KaiC phosphorylation rhythm [My Copy] Nature Structural & Molecular Biology, Vol. 14, No. 11. (28 October 2007), pp. 1084-1088. by Hiroshi Ito, Hakuto Kageyama, Michinori Mutsuda, Masato Nakajima, Tokitaka Oyama, Takao Kondo posted to circadian_rhythm by okapi on 2009-11-20 07:47:46 as
	Reconstitution of circadian oscillation of cyanobacterial KaiC phosphorylation in vitro. [My Copy] Science (New York, N.Y.), Vol. 308, No. 5720. (15 April 2005), pp. 414-415. by Masato Nakajima, Keiko Imai, Hiroshi Ito, et al.Taeko Nishiwaki, Yoriko Murayama, Hideo Iwasaki, Tokitaka Oyama, Takao Kondo posted to circadian_rhythm by okapi on 2009-11-20 07:46:40 as along with 3 people and 1 group jasonpark1 hito nasu BP205
	Myosin VI undergoes a 180Â° power stroke implying an uncoupling of the front lever arm [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 43. (27 October 2009), pp. 18255-18260. by Jeff G. Reifenberger, Erdal Toprak, HyeongJun Kim, Dan Safer, H. Lee Sweeney, Paul R. Selvin posted to myosin by okapi on 2009-11-20 07:43:24 as
	Dynamic activation of an allosteric regulatory protein [My Copy] Nature, Vol. 462, No. 7271. (19 November 2009), pp. 368-372. by Shiou-Ru Tzeng, Charalampos G. Kalodimos posted to allostery by okapi on 2009-11-20 07:40:28 as
	RNA polymerase II\|[ndash]\|TFIIB structure and mechanism of transcription initiation [My Copy] Nature, Vol. 462, No. 7271. (09 October 2009), pp. 323-330. by Dirk Kostrewa, Mirijam E. Zeller, Karim-Jean Armache, et al.Martin Seizl, Kristin Leike, Michael Thomm, Patrick Cramer posted to motor by okapi on 2009-11-20 07:39:19 as along with 3 people kintoki megraw cvaldes
	Microsecond Simulations of Spontaneous Methane Hydrate Nucleation and Growth [My Copy] Science, Vol. 326, No. 5956. (20 November 2009), pp. 1095-1098. by Matthew R. Walsh, Carolyn A. Koh, E. Dendy Sloan, Amadeu K. Sum, David T. Wu posted to simulation by okapi on 2009-11-20 07:36:23 as
	Predicting new molecular targets for known drugs [My Copy] Nature, Vol. 462, No. 7270. (01 November 2009), pp. 175-181. by Michael J. Keiser, Vincent Setola, John J. Irwin, et al.Christian Laggner, Atheir I. Abbas, Sandra J. Hufeisen, Niels H. Jensen, Michael B. Kuijer, Roberto C. Matos, Thuy B. Tran, Ryan Whaley, Richard A. Glennon, Jerome Hert, Kelan L. H. Thomas, Douglas D. Edwards, Brian K. Shoichet, Bryan L. Roth posted to drug_design by okapi on 2009-11-15 10:11:08 as along with 14 people and 1 group venancio ahmetbakan zufar pablocarb zwang TRHvidsten phoenixzxl qshao Yanno mnishimu tmmurali sjcockell seb1 abhishek_tiwari Journal picks
	Drug discovery: Predicting promiscuity [My Copy] Nature, Vol. 462, No. 7270. (11 November 2009), pp. 167-168. by Andrew L. Hopkins posted to drug_design by okapi on 2009-11-15 10:09:57 as along with 1 person pablocarb
	Paddling mechanism for the substrate translocation by AAA+ motor revealed by multiscale molecular simulations [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 43. (27 October 2009), pp. 18237-18242. by Nobuyasu Koga, Tomoshi Kameda, Kei-ichi Okazaki, Shoji Takada posted to simulation multiscale motor by okapi on 2009-11-04 08:39:29 as
	Enzyme millisecond conformational dynamics do not catalyze the chemical step [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 41. (13 October 2009), pp. 17359-17364. by Andrei V. Pisliakov, Jie Cao, Shina C. L. Kamerlin, Arieh Warshel posted to conformational_dynamics allostery by okapi on 2009-10-17 17:57:36 as along with 1 person jjray
	Cargo binding induces dimerization of myosin VI [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 41. (13 October 2009), pp. 17320-17324. by Denis Phichith, Mirko Travaglia, Zhaohui Yang, et al.Xiaoyan Liu, Alan B. Zong, Daniel Safer, H. Lee Sweeney posted to myosin by okapi on 2009-10-17 17:53:18 as along with 1 person richardfranzese
	Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 9. (8 September 2009), pp. 2531-2543. by Xavier Periole, Marco Cavalli, Siewert-Jan Marrink, Marco A. Ceruso posted to multiscale by okapi on 2009-09-26 16:01:36 as along with 3 people and 2 groups TonyIvetac pmung A_Coletta_Thesis McCammon Structural Biology Group TorVergata
	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 multiscale by okapi on 2009-09-26 15:17:11 as along with 4 people and 3 groups anuragsethi barry sobolevnrm apaydin structural_bioinformatics McCammon baker-group
	Coarse-grained modeling of allosteric regulation in protein receptors [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 34. (25 August 2009), pp. 14253-14258. by Ilya A. Balabin, Weitao Yang, David N. Beratan posted to coarse-grain allostery by okapi on 2009-08-26 12:21:59 as along with 4 people and 1 group sobolevnrm pmung jmccammon agrossfield 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 allostery by okapi on 2009-08-26 12:20:37 as along with 5 people and 1 group ahmetbakan apaydin anuragsethi jmccammon boris_aguilar McCammon
	The origin of allosteric functional modulation: multiple pre-existing pathways. [My Copy] Structure (London, England : 1993), Vol. 17, No. 8. (12 August 2009), pp. 1042-1050. by Antonio del Sol, Chung-Jung J. Tsai, Buyong Ma, Ruth Nussinov posted to allostery by okapi on 2009-08-22 16:02:41 as along with 4 people and 2 groups ubcg08l higueruelo pablocarb barry structural_bioinformatics McCammon
	A Systematic Methodology for Defining Coarse-Grained Sites in Large Biomolecules [My Copy] Biophysical Journal, Vol. 95, No. 11. (01 December 2008), pp. 5073-5083. by Z. Zhang, L. Lu, W. Noid, V. Krishna, J. Pfaendtner, G. Voth posted to multiscale by okapi on 2009-08-22 15:54:12 as along with 5 people and 2 groups barry sobolevnrm choonpeng agrossfield paulschlesinger structural_bioinformatics McCammon
	Nucleotide-dependent conformational states of actin [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 31. (4 August 2009), pp. 12723-12728. by Jim Pfaendtner, Davide Branduardi, Michele Parrinello, Thomas D. Pollard, Gregory A. Voth posted to allostery by okapi on 2009-08-22 15:45:38 as along with 3 people and 2 groups pmung anuragsethi barry structural_bioinformatics McCammon
	Visualizing myosin–actin interaction with a genetically-encoded fluorescent strain sensor [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 44. (4 November 2008), pp. 16882-16887. by Sosuke Iwai, Taro Q. Uyeda posted to myosin by okapi on 2009-05-27 11:00:10 as along with 3 people and 1 group cactus barry melting McCammon
	Allosteric Communication in Myosin V: From Small Conformational Changes to Large Directed Movements [My Copy] PLoS Comput Biol, Vol. 4, No. 8. (2008), e1000129. by M. Cecchini, A. Houdusse, M. Karplus posted to myosin by okapi on 2009-05-27 10:57:27 as along with 2 people aqeel barry
	Extensive Conformational Transitions Are Required to Turn On ATP Hydrolysis in Myosin [My Copy] Journal of Molecular Biology, Vol. 381, No. 5. (19 September 2008), pp. 1407-1420. by Yang Yang, Haibo Yu, Qiang Cui posted to myosin by okapi on 2009-05-27 10:56:18 as along with 1 person and 2 groups barry Bioinformatics structural_bioinformatics
	Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. [My Copy] J Mol Biol, Vol. 256, No. 3. (1 March 1996), pp. 623-644. by S. Miyazawa, R. L. Jernigan posted to binding by okapi on 2009-05-06 14:24:49 as along with 4 people and 1 group krapnik choonpeng rabio joseph_x_zhou protein_Dyn
	Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 32. (12 August 2008), pp. 11182-11187. by Kei-ichi Okazaki, Shoji Takada posted to allostery by okapi on 2009-05-06 14:16:27 as along with 8 people and 2 groups oteri bmduggan xdeupi aqeel raik ruvido barry zwang structural_bioinformatics McCammon
	Coarse-grained Models for Simulations of Multiprotein Complexes: Application to Ubiquitin Binding [My Copy] Journal of Molecular Biology, Vol. 375, No. 5. (01 February 2008), pp. 1416-1433. by Young C. Kim, Gerhard Hummer posted to binding by okapi on 2009-05-06 14:12:56 as along with 4 people and 3 groups barry sobolevnrm iantunbridge mikaellund structural_bioinformatics Bioinformatics baker-group
	Replica exchange simulations of transient encounter complexes in protein–protein association [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 35. (2 September 2008), pp. 12855-12860. by Young C. Kim, Chun Tang, G. Marius Clore, Gerhard Hummer posted to binding by okapi on 2009-05-06 14:07:15 as along with 2 people and 2 groups barry cactus structural_bioinformatics McCammon
	GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation [My Copy] Journal of Chemical Theory and Computation, Vol. 4, No. 3. (1 March 2008), pp. 435-447. by B. Hess, C. Kutzner, D. van der Spoel, E. Lindahl posted to simulation by okapi on 2009-03-16 12:02:22 as along with 23 people and 2 groups sunnytov softsimu parnell rabio oteri krapnik robertvacha rodrigofaccioli pavanghatty janneb ZhangYinhe flbarroso marceavi A_Coletta_Thesis choonpeng Lombardo_7 jwm daevans mmuecke sobolevnrm r2s2 middledomain loison Structural Biology Group TorVergata baker-group
	Single-molecule experiments in vitro and in silico. [My Copy] Science, Vol. 316, No. 5828. (25 May 2007), pp. 1144-1148. by M. Sotomayor, K. Schulten posted to simulation by okapi on 2009-03-16 11:50:00 as along with 4 people and 1 group devinli choonpeng skoch3 hsekiguc Koch_Lab
	Intersubunit coordination in a homomeric ring ATPase [My Copy] Nature (07 January 2009) by Jeffrey R. Moffitt, Yann R. Chemla, K. Aathavan, et al.Shelley Grimes, Paul J. Jardine, Dwight L. Anderson, Carlos Bustamante posted to f1-atpase by okapi on 2009-03-16 11:47:25 as along with 4 people hsekiguc devinli cactus melting
	Axle-Less F1-ATPase Rotates in the Correct Direction [My Copy] Science, Vol. 319, No. 5865. (15 February 2008), pp. 955-958. by Shou Furuike, Mohammad D. Hossain, Yasushi Maki, et al.Kengo Adachi, Toshiharu Suzuki, Ayako Kohori, Hiroyasu Itoh, Masasuke Yoshida, Kazuhiko Kinosita posted to f1-atpase by okapi on 2009-03-16 11:37:43 as along with 3 people hsekiguc cactus melting
	Ligand-Dependent Equilibrium Fluctuations of Single Calmodulin Molecules [My Copy] Science, Vol. 323, No. 5914. (30 January 2009), pp. 633-637. by Jan P. Junker, Fabian Ziegler, Matthias Rief posted to allostery by okapi on 2009-02-02 06:36:40 as along with 3 people kjell hsekiguc flbarroso
	BIOCHEMISTRY: Unfolding the Secrets of Calmodulin [My Copy] Science, Vol. 323, No. 5914. (30 January 2009), pp. 593-594. by Robert B. Best, Gerhard Hummer posted to allostery by okapi on 2009-02-02 06:32:28 as along with 1 person flbarroso

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okapi's library 40 articles Export

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