hmk's alternatives [16 articles] Export

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

	Generalized ensemble methods for de novo structure prediction [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 5. (3 February 2009), pp. 1415-1420. by Alena Shmygelska, Michael Levitt posted to alternatives data decoy protein_structure by hmk on 2009-02-03 23:17:08 as along with 6 people mijam rabio kentsis apaydin nurban amishp
	Algorithm for backrub motions in protein design [My Copy] Bioinformatics, Vol. 24, No. 13. (1 July 2008), pp. i196-204. by Ivelin Georgiev, Daniel Keedy, Jane S. Richardson, David C. Richardson, Bruce R. Donald posted to alternatives backbone backrub code data protein_design protein_structure by hmk on 2008-12-25 22:07:11 as along with 2 people dfgreen jwm
	Structure - Predicting the Energetics of Conformational Fluctuations in Proteins from Sequence: A Strategy for Profiling the Proteome [My Copy] posted to alternatives conformational_entropy data free_energy protein_structure by hmk on 2008-11-12 20:51:40 as
	Predicting the reactivity of proteins from their sequence alone: Kazal family of protein inhibitors of serine proteinases [My Copy] PNAS, Vol. 98, No. 4. (13 February 2001), pp. 1410-1415. by Stephen M. Lu, Wuyuan Lu, M. A. Qasim, et al.Stephen Anderson, Izydor Apostol, Wojciech Ardelt, Theresa Bigler, Yi W. Chiang, James Cook, Michael N. James, Ikunoshin Kato, Clyde Kelly, William Kohr, Tomoko Komiyama, Tiao-Yin Lin, Michio Ogawa, Jacek Otlewski, Soon-Jae Park, Sabiha Qasim, Michael Ranjbar, Misao Tashiro, Nicholas Warne, Harry Whatley, Anna Wieczorek, Maciej Wieczorek, Tadeusz Wilusz, Richard Wynn, Wenlei Zhang, Michael Laskowski posted to alternatives data free_energy protein_protein_interactions by hmk on 2008-10-01 02:08:46 as along with 2 people apaydin softsimu
	Flexibility and conformational entropy in protein-protein binding. [My Copy] Structure, Vol. 14, No. 4. (April 2006), pp. 683-693. by R. Grünberg, M. Nilges, J. Leckner posted to alternatives analysis backbone data entropy free_energy protein_protein_interactions side_chain_prediction by hmk on 2008-09-28 17:38:05 as along with 6 people and 2 groups raik barry pansapiens lna aqeel allmensch structural_bioinformatics Bioinformatics
	Free Energy Decomposition of Protein-Protein Interactions [My Copy] Biophys. J., Vol. 81, No. 2. (1 August 2001), pp. 737-750. by Sergey Y. Noskov, Carmay Lim posted to alternatives analysis binding data free_energy protein_protein_interactions protein_structure by hmk on 2008-09-28 17:35:10 as
	Toward rational protein crystallization: A Web server for the design of crystallizable protein variants [My Copy] Protein Sci, Vol. 16, No. 8. (1 August 2007), pp. 1569-1576. by Lukasz Goldschmidt, David R. Cooper, Zygmunt S. Derewenda, David Eisenberg posted to alternatives data entropy protein_design protein_structure by hmk on 2008-08-21 20:49:44 as
	Thermodynamic basis of resistance to HIV-1 protease inhibition: calorimetric analysis of the V82F/I84V active site resistant mutant. [My Copy] Biochemistry, Vol. 39, No. 39. (3 October 2000), pp. 11876-11883. by M. J. Todd, I. Luque, A. Velázquez-Campoy, E. Freire posted to alternatives data drug_design hiv hivpr protein_structure by hmk on 2008-07-08 15:27:35 as
	A simple physical model for binding energy hot spots in proteinâprotein complexes [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 22. (29 October 2002), pp. 14116-14121. by Tanja Kortemme, David Baker posted to alternatives data free_energy molecular_mechanics protein_protein_interactions by hmk on 2008-06-01 00:24:36 as along with 8 people and 1 group chemrahul82 onufriev oceanwind lna jwm bicko cjeans skoddet Nielsen group
	Calculation of protein-ligand binding affinities. [My Copy] Annual review of biophysics and biomolecular structure, Vol. 36 (2007), pp. 21-42. by Michael K. Gilson, Huan-Xiang X. Zhou posted to alternatives binding data free_energy by hmk on 2008-04-03 20:50:50 as along with 15 people and 3 groups mijogiffin flbarroso GermanErlenkamp onufriev arlam oteri jmccammon bmduggan dimka neils ashaytan ras cchang boris_aguilar qaiser_fatmi Chang group Structural Biology Group TorVergata McCammon
	Framework for kernel regularization with application to protein clustering [My Copy] Proceedings of the National Academy of Sciences, Vol. 102, No. 35. (30 August 2005), pp. 12332-12337. by Fan Lu, Sunduz Keles, Stephen J. Wright, Grace Wahba posted to alternatives data dynamics molecular_dynamics protein_structure by hmk on 2007-12-25 01:10:04 as
	Can a physics-based, all-atom potential find a protein's native structure among misfolded structures? I. Large scale AMBER benchmarking [My Copy] Journal of Computational Chemistry, Vol. 28, No. 12. (2007), pp. 2059-2066. by Liliana Wroblewska, Jeffrey Skolnick posted to alternatives data decoy decoy_detection free_energy molecular_dynamics by hmk on 2007-12-12 16:49:46 as along with 1 person pawelp
	Computational design of protein-protein interactions. [My Copy] Current opinion in chemical biology, Vol. 8, No. 1. (February 2004), pp. 91-97. by Tanja Kortemme, David Baker posted to alternatives data molecular_mechanics physics protein_protein_interactions by hmk on 2007-12-12 15:44:14 as along with 7 people bmduggan qluo lna jwm bicko cjeans jteyra
	Wordom: a program for efficient analysis of molecular dynamics simulations [My Copy] Bioinformatics, Vol. 23, No. 19. (1 October 2007), pp. 2625-2627. by Michele Seeber, Marco Cecchini, Francesco Rao, Giovanni Settanni, Amedeo Caflisch posted to alternatives molecular_dynamics protein_folding by hmk on 2007-12-09 05:02:58 as along with 6 people and 2 groups guhjy barry tmmurali choonpeng sobolevnrm LamBras structural_bioinformatics baker-group
	Coarse-Grained Biomolecular Simulation with REACH: Realistic Extension Algorithm via Covariance Hessian☆ [My Copy] Biophysical Journal, Vol. 93, No. 10. (15 November 2007), pp. 3460-3469. by K. Moritsugu, J. Smith posted to alternatives graphical_models molecular_dynamics protein_folding by hmk on 2007-12-09 03:09:17 as along with 5 people and 1 group edws Diego_Prada aqeel sobolevnrm choonpeng baker-group
	High-throughput modeling and analysis of protein structural dynamics [My Copy] Brief Bioinform, Vol. 8, No. 6. (1 November 2007), pp. 432-445. by Xiong Liu, Hassan A. Karimi posted to alternatives data molecular_dynamics protein_structure by hmk on 2007-12-09 02:50:59 as along with 1 person aqeel

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protein_structure	58
free_energy	32
data	29
graphical_models	17
alternatives	16
decoy_detection	13
molecular_dynamics	12
protein_protein_interactions	11
molecular_mechanics	11
physics	10
inference	9
docking	8
side_chain_prediction	8
statistics	8
entropy	6
protein_design	6
protein_folding	6
decoy	4
protein_fold	4
dynamics	4
hivpr	3
hiv	3
binding	3
ensemble	3
drug_design	3
nmr	2
marginal_map	2
review	2
symbolic_encoding	2
conformational_entropy	2
industry	2
backbone	2
rotamer_library	2
systems_biology	2
analysis	2
continuous_model	1
crf	1
challenges	1
quantum_physics	1
library	1
protein_dna	1
math	1
probability	1
code	1
information_theory	1
hivprdata	1
advice	1
pharma	1
mcmc	1
drug_discovery	1
allostery	1
loops	1
ligand_binding	1
backrub	1
jaynes	1
genetics	1
sampling	1
camp	1

hmk's alternatives [16 articles] Export

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