hmk's free_energy [32 articles] Export

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	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
	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
	A simple physical model for binding energy hot spots in protein-protein 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 7 people and 1 group onufriev oceanwind lna jwm bicko cjeans skoddet Nielsen group
	Unified Approach for Molecular Dynamics and Density-Functional Theory [My Copy] Physical Review Letters, Vol. 55, No. 22. (Nov 1985), pp. 2471-2474. by R. Car, M. Parrinello posted to free_energy molecular_dynamics physics quantum_physics by hmk on 2008-04-10 07:07:29 as along with 5 people and 1 group moldyn_ich whitead gferencz and_ped10 eyliu Jiang Research Group
	"Mining Minima": Direct Computation of Conformational Free Energy [My Copy] J. Phys. Chem. A, Vol. 101, No. 8. (20 February 1997), pp. 1609-1618. by M. S. Head, J. A. Given, M. K. Gilson posted to free_energy by hmk on 2008-04-03 20:52:59 as
	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
	Extraction of configurational entropy from molecular simulations via an expansion approximation [My Copy] The Journal of Chemical Physics, Vol. 127, No. 2. (2007) by Benjamin J. Killian, Joslyn Y. Kravitz, Michael K. Gilson posted to free_energy protein_structure by hmk on 2008-04-03 20:46:55 as along with 1 person and 1 group arlam Chang group
	A new class of models for computing receptor-ligand binding affinities [My Copy] Chemistry & Biology, Vol. 4, No. 2. (1997), pp. 87-92. by Michael K. Gilson, James A. Given, Martha S. Head posted to free_energy molecular_dynamics protein_protein_interactions by hmk on 2008-04-03 20:40:59 as
	The statistical-thermodynamic basis for computation of binding affinities: a critical review. [My Copy] Biophys J, Vol. 72, No. 3. (March 1997), pp. 1047-1069. by M. K. Gilson, J. A. Given, B. L. Bush, J. A. McCammon posted to entropy free_energy molecular_dynamics physics protein_structure review by hmk on 2008-04-03 20:07:07 as along with 3 people and 2 groups dfgreen ssomani cchang structure-bii Chang group
	Spotlight: Computational Biology at the Beginning of the Post-genomic Era Thomas Lengauer [My Copy] posted to challenges free_energy by hmk on 2008-04-03 20:06:14 as
	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
	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
	Construction of effective free energy landscape from single-molecule time series [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 49. (4 December 2007), pp. 19297-19302. by Akinori Baba, Tamiki Komatsuzaki posted to free_energy graphical_models protein_folding protein_structure by hmk on 2007-12-07 03:49:47 as along with 6 people and 1 group zwang cactus sobolevnrm Diego_Prada arnaudriegert hsekiguc baker-group
	Protein Free Energy Landscapes Remodeled by Ligand Binding [My Copy] Biophys. J., Vol. 93, No. 2. (15 July 2007), pp. 579-585. by Troy C. Messina, David S. Talaga posted to free_energy graphical_models protein_folding protein_structure by hmk on 2007-12-07 03:46:10 as
	Large-scale characteristics of the energy landscape in protein-protein interactions. [My Copy] Proteins (11 October 2007) by Nicholas O'toole, Ilya A A. Vakser posted to free_energy protein_folding protein_protein_interactions protein_structure by hmk on 2007-12-06 07:18:22 as along with 2 people bicko paulschlesinger
	Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction [My Copy] PNAS, Vol. 103, No. 26. (27 June 2006), pp. 9885-9890. by Payel Das, Mark Moll, Hernan Stamati, Lydia E. Kavraki, Cecilia Clementi posted to dynamics free_energy graphical_models protein_folding by hmk on 2007-12-06 00:10:32 as along with 2 people and 2 groups samjlord sobolevnrm moernerlab baker-group
	Sampling Realistic Protein Conformations Using Local Structural Bias. [My Copy] PLoS Comput Biol, Vol. 2, No. 9. (22 September 2006) by Thomas Hamelryck, John T T. Kent, Anders Krogh posted to free_energy graphical_models protein_fold protein_structure statistics by hmk on 2007-10-31 17:54:26 as along with 3 people xingwuliu wouterboomsma j3xucite
	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
	Recognition of errors in three-dimensional structures of proteins. [My Copy] Proteins, Vol. 17, No. 4. (December 1993), pp. 355-362. by M. J. Sippl posted to decoy_detection free_energy graphical_models by hmk on 2007-04-28 23:50:26 as along with 2 people medic0747 j3xucite
	Modeling protein conformational ensembles: From missing loops to equilibrium fluctuations [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 65, No. 1. (2006), pp. 164-179. by Amarda Shehu, Cecilia Clementi, Lydia E. Kavraki posted to free_energy loops protein_structure by hmk on 2007-03-23 01:39:24 as along with 6 people and 2 groups apaydin nigham aqeel yongzhao elham sobolevnrm TSRI_MGL baker-group
	Structural stability of oligomeric proteins: A mean-field theoretical approach [My Copy] Journal of Computer-Aided Materials Design, Vol. V4, No. 1. (1 April 1997), pp. 1-8. by Armin R. Vã¶lkel, Jaan Noolandi posted to free_energy inference protein_structure by hmk on 2007-03-09 00:04:55 as
	Streptavidin Tetramerization and 2D Crystallization: A Mean-Field Approach [My Copy] Biophys. J., Vol. 80, No. 4. (1 April 2001), pp. 2004-2010. by T. Coussaert, A. R. Volkel, J. Noolandi, A. P. Gast posted to free_energy graphical_models inference protein_structure by hmk on 2007-03-09 00:01:52 as
	The Cluster Variation Method for Efficient Linkage Analysis on Extended Pedigrees [My Copy] BMC Bioinformatics, Vol. 7, No. Suppl 1. (2006) by Cornelis Albers, Martijn Leisink, Hilbert Kappen posted to free_energy graphical_models by hmk on 2007-03-07 02:40:46 as
	Flexibility and packing in proteins [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 3. (5 February 2002), pp. 1274-1279. by Bertil Halle posted to free_energy protein_structure by hmk on 2007-02-23 23:57:08 as along with 7 people and 3 groups Diego_Prada edws barry sobolevnrm ana aqeel allmensch baker-group structural_bioinformatics Bioinformatics
	Decomposition of the Free Energy of a System in Terms of Specific Interactions : Implications for Theoretical and Experimental Studies [My Copy] Journal of Molecular Biology, Vol. 240, No. 2. (7 July 1994), pp. 167-176. by Alan E. Mark, Wilfred F. van Gunsteren posted to docking free_energy protein_structure by hmk on 2007-02-23 16:39:50 as
	Thermodynamics of the interaction of barnase and barstar: changes in free energy versus changes in enthalpy on mutation [My Copy] Journal of Molecular Biology, Vol. 267, No. 3. (4 April 1997), pp. 696-706. by Christian Frisch, Gideon Schreiber, Christopher M. Johnson, Alan R. Fersht posted to docking free_energy protein_structure by hmk on 2007-02-23 16:26:49 as
	Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. [My Copy] J Mol Biol, Vol. 320, No. 2. (5 July 2002), pp. 369-387. by R. Guerois, J. E. Nielsen, L. Serrano posted to protein_structure free_energy by hmk on 2007-02-23 14:53:30 as along with 4 people apaydin aalibes chad_davis carlescorbi

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

hmk's free_energy [32 articles] Export

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