hmk's data [29 articles] Export

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	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
	Frequent polymorphism at drug resistance sites in HIV-1 protease and reverse transcriptase. [My Copy] AIDS (London, England), Vol. 22, No. 4. (19 February 2008), pp. 497-501. by M. Kearney, S. Palmer, F. Maldarelli, et al.W. Shao, M. A. Polis, J. Mican, D. Rock-Kress, J. B. Margolick, J. M. Coffin, J. W. Mellors posted to data hivpr by hmk on 2009-01-17 22:06:14 as along with 1 person mishar
	Literature-curated protein interaction datasets [My Copy] Nature Methods, Vol. 6, No. 1. (30 December 2008), pp. 39-46. by Michael E. Cusick, Haiyuan Yu, Alex Smolyar, et al.Kavitha Venkatesan, Anne-Ruxandra Carvunis, Nicolas Simonis, Jean-Francois Rual, Heather Borick, Pascal Braun, Matija Dreze, Jean Vandenhaute, Mary Galli, Junshi Yazaki, David E. Hill, Joseph R. Ecker, Frederick P. Roth, Marc Vidal posted to data protein_protein_interactions by hmk on 2009-01-02 23:16:04 as along with 16 people aceol fgibson allysonlister carlk aramesh2 ocs reyez kshameer neils daforerog lesikv sjcockell dullhunk icq242500260 guhjy zwang
	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
	Entropy Calculation of HIV-1 Env gp120, its Receptor CD4, and their Complex: An Analysis of Configurational Entropy Changes upon Complexation [My Copy] Biophys. J., Vol. 88, No. 1. (1 January 2005), pp. 15-24. by Shang-Te D. Hsu, Christine Peter, Wilfred F. van Gunsteren, Alexandre M. Bonvin posted to binding conformational_entropy data entropy free_energy hiv protein_structure by hmk on 2008-09-18 00:38:08 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
	Stability of 100 homo and heterotypic coiled-coil a-a' pairs for ten amino acids (A, L, I, V, N, K, S, T, E, and R). [My Copy] Biochemistry, Vol. 45, No. 38. (26 September 2006), pp. 11324-11332. by A. Acharya, V. Rishi, C. Vinson posted to data free_energy protein_protein_interactions by hmk on 2008-08-21 20:35:33 as along with 6 people kgutwin gwenknight chgjb kevinchannon bethbromley ca3295
	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
	Kinetic characterization and cross-resistance patterns of HIV-1 protease mutants selected under drug pressure. [My Copy] Biochemistry, Vol. 34, No. 29. (25 July 1995), pp. 9282-9287. by S. V. Gulnik, L. I. Suvorov, B. Liu, et al.B. Yu, B. Anderson, H. Mitsuya, J. W. Erickson posted to data drug_design hiv hivpr protein_structure by hmk on 2008-07-08 15:25:51 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
	Calculation of the Entropy and Free Energy from Monte Carlo Simulations of a Peptide Stretched by an External Force [My Copy] J. Phys. Chem. B, Vol. 109, No. 46. (24 November 2005), pp. 21963-21970. by S. Cheluvaraja, H. Meirovitch posted to data entropy free_energy molecular_dynamics protein_structure by hmk on 2008-04-03 19:54:33 as
	The atomic structure of protein-protein recognition sites [My Copy] Journal of Molecular Biology, Vol. 285, No. 5. (5 February 1999), pp. 2177-2198. by Loredana L. Conte, Cyrus Chothia, Joel Janin posted to data free_energy graphical_models protein_protein_interactions by hmk on 2008-03-15 22:31:01 as
	On Design of Optimal Nonlinear Kernel Potential Function for Protein Folding and Protein Design [My Copy] by Changyu Hu, Xiang Li, Jie Liang posted to data decoy decoy_detection molecular_mechanics protein_design protein_structure by hmk on 2008-01-06 00:26:29 as
	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
	A consensus view of fold space: combining SCOP, CATH, and the Dali Domain Dictionary. [My Copy] Protein science : a publication of the Protein Society, Vol. 12, No. 10. (October 2003), pp. 2150-2160. by Ryan Day, David A. Beck, Roger S. Armen, Valerie Daggett posted to data protein_fold protein_structure by hmk on 2007-12-09 05:38:39 as along with 6 people and 2 groups HawkinsJohnC dfdong ana barry tjimenez dimka structural_bioinformatics Bioinformatics
	Ensemble versus single-molecule protein unfolding. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 38. (20 September 2005), pp. 13445-13450. by R. Day, V. Daggett posted to data ensemble molecular_dynamics by hmk on 2007-12-09 05:25:34 as along with 2 people bilab choonpeng
	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
	A consensus view of protein dynamics [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 3. (16 January 2007), pp. 796-801. by Manuel Rueda, Carles Ferrer-Costa, Tim Meyer, et al.Alberto Pérez, Jordi Camps, Adam Hospital, Josep L. Gelpí, Modesto Orozco posted to data dynamics graphical_models molecular_dynamics by hmk on 2007-12-09 02:49:20 as along with 14 people and 1 group Diego_Prada bmduggan lna dimka aqeel aswin rabio grahamc zwang biehl Ema phoenixzxl ras LamBras The BMM Dome
	Computational design of antibody-affinity improvement beyond in vivo maturation. [My Copy] Nat Biotechnol (23 September 2007) by Shaun M M. Lippow, K Dane D. Wittrup, Bruce Tidor posted to data free_energy graphical_models protein_design protein_fold protein_structure by hmk on 2007-10-31 14:06:33 as along with 4 people and 1 group Scis0000002 kirasato dfgreen zwang Chang group
	Toward high-resolution prediction and design of transmembrane helical protein structures [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 40. (2 October 2007), pp. 15682-15687. by P. Barth, J. Schonbrun, D. Baker posted to data decoy_detection molecular_mechanics physics protein_structure by hmk on 2007-10-02 22:57:07 as along with 3 people zwang biehl Ema
	Diverse, High-Quality Test Set for the Validation of Protein−Ligand Docking Performance [My Copy] Journal of Medicinal Chemistry, Vol. 50, No. 4. (1 February 2007), pp. 726-741. by Michael J. Hartshorn, Marcel L. Verdonk, Gianni Chessari, et al.Suzanne C. Brewerton, Wijnand T. M. Mooij, Paul N. Mortenson, Christopher W. Murray posted to data decoy_detection docking by hmk on 2007-03-30 17:55:36 as along with 9 people flbarroso GermanErlenkamp massivemayhem higueruelo BragilMassoud daevans ramensky superpyrin thanatos
	Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. [My Copy] J Mol Biol, Vol. 331, No. 1. (1 August 2003), pp. 281-299. by J. J. Gray, S. Moughon, C. Wang, et al.O. Schueler-Furman, B. Kuhlman, C. A. Rohl, D. Baker posted to data decoy_detection docking protein_structure by hmk on 2007-03-02 22:35:12 as along with 2 people oceanwind jwm

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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 data [29 articles] Export

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