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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
	Identification of direct residue contacts in protein–protein interaction by message passing [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 1. (6 January 2009), pp. 67-72. by Martin Weigt, Robert A. White, Hendrik Szurmant, James A. Hoch, Terence Hwa posted to graphical_models inference protein_protein_interactions protein_structure by hmk on 2009-01-07 06:08:31 as along with 6 people and 2 groups orr cactus haisent sobolevnrm sjcockell akraemer KeatingJClub baker-group
	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
	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
	Insights into Protein–DNA Interactions through Structure Network Analysis [My Copy] PLoS Comput Biol, Vol. 4, No. 9. (2008), e1000170. by R. Sathyapriya, M. S. Vijayabaskar, Saraswathi Vishveshwara posted to molecular_mechanics physics protein_dna protein_structure by hmk on 2008-09-05 16:28:42 as along with 9 people and 1 group TRHvidsten svozil Zephyrus Ema emptyhb aalibes AbnerCYH Totobox zwang Roswell Cancer Crosstalk
	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
	Protein Side-Chain Placement Through MAP Estimation and Problem-Size Reduction, [My Copy] In 6th Workshop on Algorithms in Bioinformatics (WABI) 2006, pp. 219-230. posted to graphical_models inference protein_design protein_structure side_chain_prediction by hmk on 2008-07-20 15:54:09 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
	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
	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
	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
	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
	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
	A consensus view of fold space: combining SCOP, CATH, and the Dali Domain Dictionary. [My Copy] Protein Sci, Vol. 12, No. 10. (October 2003), pp. 2150-2160. by R. Day, D. A. Beck, R. S. Armen, V. Daggett posted to data protein_fold protein_structure by hmk on 2007-12-09 05:38:39 as along with 5 people and 2 groups dfdong ana barry tjimenez dimka structural_bioinformatics Bioinformatics
	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
	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 7 people and 1 group victorclaessen 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
	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
	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
	All are not equal: A benchmark of different homology modeling programs [My Copy] Protein Sci, Vol. 14, No. 5. (1 May 2005), pp. 1315-1327. by Bjorn Wallner, Arne Elofsson posted to protein_structure side_chain_prediction by hmk on 2007-04-10 21:39:25 as along with 6 people and 2 groups cdeane karbak marcius eweaver BioNica rsantana BioinfoCIPF SGU-CIPF
	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
	An Orientation-dependent Hydrogen Bonding Potential Improves Prediction of Specificity and Structure for Proteins and Protein-Protein Complexes [My Copy] Journal of Molecular Biology, Vol. 326, No. 4. (28 February 2003), pp. 1239-1259. by Tanja Kortemme, Alexandre V. Morozov, David Baker posted to molecular_mechanics physics protein_structure side_chain_prediction by hmk on 2007-03-15 20:47:05 as along with 3 people krapnik Elena_Zubova mirzazadeh
	Design of a novel globular protein fold with atomic-level accuracy. [My Copy] Science (New York, N.Y.), Vol. 302, No. 5649. (21 November 2003), pp. 1364-1368. by Brian Kuhlman, Gautam Dantas, Gregory C. Ireton, Gabriele Varani, Barry L. Stoddard, David Baker posted to graphical_models molecular_mechanics physics protein_design protein_structure by hmk on 2007-03-14 01:23:38 as along with 10 people bmduggan kgutwin Diego_Prada onufriev apaydin dfgreen jwm heymiki kevinchannon ca3295
	Effective energy function for proteins in solution. [My Copy] Proteins, Vol. 35, No. 2. (1 May 1999), pp. 133-152. by T. Lazaridis, M. Karplus posted to molecular_mechanics physics protein_structure by hmk on 2007-03-13 18:18:43 as along with 6 people and 2 groups melo_mcr oceanwind marcius bluvsh1 choonpeng kgutwin BioinfoCIPF SGU-CIPF
	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
	Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and bayesian scoring functions [My Copy] Journal of Molecular Biology, Vol. 268, No. 1. (25 April 1997), pp. 209-225. by K. Simons posted to decoy_detection protein_structure by hmk on 2007-03-03 20:47:53 as along with 12 people and 2 groups chemrahul82 paddydu Diego_Prada reyez guxiyou ana jwm vavi wouterboomsma j3xucite mijam joule structural_bioinformatics Bioinformatics
	Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins [My Copy] Proteins: Structure, Function, and Genetics, Vol. 34, No. 1. (1999), pp. 82-95. by Kim T. Simons, Ingo Ruczinski, Charles Kooperberg, Brian A. Fox, Chris Bystroff, David Baker posted to decoy_detection protein_structure by hmk on 2007-03-03 20:45:55 as along with 2 people paddydu bpb
	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
	Improved side-chain modeling for protein-protein docking. [My Copy] Protein Sci, Vol. 14, No. 5. (May 2005), pp. 1328-1339. by C. Wang, O. Schueler-Furman, D. Baker posted to decoy_detection docking protein_structure by hmk on 2007-03-02 22:33:34 as along with 11 people and 3 groups dgront csrocha barry aqeel jwm bicko yongzhao blackbart bluvsh1 selrac Evangelia structural_bioinformatics Bioinformatics TSRI_MGL
	Influence of protein structure databases on the predictive power of statistical pair potentials [My Copy] Proteins: Structure, Function, and Genetics, Vol. 31, No. 2. (1998), pp. 139-149. by Emiko Furuichi, Patrice Koehl posted to decoy_detection protein_structure by hmk on 2007-02-27 22:16:10 as
	Near-native structure refinement using in vacuo energy minimization [My Copy] PNAS, Vol. 104, No. 9. (27 February 2007), pp. 3177-3182. by Christopher M. Summa, Michael Levitt posted to decoy_detection protein_structure by hmk on 2007-02-27 18:54:39 as along with 2 people mijam thaliana
	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
	The molecular architecture of protein-protein binding sites. [My Copy] Current opinion in structural biology, Vol. 17, No. 1. (February 2007), pp. 67-76. by Dana Reichmann, Ofer Rahat, Mati Cohen, Hani Neuvirth, Gideon Schreiber posted to docking protein_structure by hmk on 2007-02-23 14:55:48 as along with 6 people allmensch laurabailey bicko choonpeng higueruelo marti
	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
	Bayesian statistical analysis of protein side-chain rotamer preferences. [My Copy] Protein Sci, Vol. 6, No. 8. (August 1997), pp. 1661-1681. by R. L. Dunbrack, F. E. Cohen posted to protein_structure side_chain_prediction by hmk on 2007-02-12 18:29:57 as along with 12 people and 2 groups karbak nknii j3xucite dgront blackbart kazemi rsantana LamBras mijam jwm phoenixzxl zwang MuraLab TCR_Signaling
	SMoS: a database of structural motifs of protein superfamilies [My Copy] Protein Eng., Vol. 16, No. 11. (1 November 2003), pp. 791-793. by Saikat Chakrabarti, K. Venkatramanan, R. Sowdhamini posted to protein_structure protein_fold by hmk on 2007-02-09 15:39:59 as
	Ab initio protein structure prediction of CASP III targets using ROSETTA [My Copy] Proteins: Structure, Function, and Genetics, Vol. 37, No. S3. (1999), pp. 171-176. by Kim T. Simons, Rich Bonneau, Ingo Ruczinski, David Baker posted to protein_structure decoy_detection by hmk on 2007-02-08 23:26:18 as
	Modeling structurally variable regions in homologous proteins with rosetta. [My Copy] Proteins, Vol. 55, No. 3. (15 May 2004), pp. 656-677. by C. A. Rohl, C. E. Strauss, D. Chivian, D. Baker posted to protein_structure molecular_mechanics by hmk on 2007-02-08 23:25:10 as along with 4 people and 1 group jwm vavi yongzhao thamelry TSRI_MGL
	Force fields for protein simulations. [My Copy] Adv Protein Chem, Vol. 66 (2003), pp. 27-85. by J. W. Ponder, D. A. Case posted to protein_structure molecular_mechanics by hmk on 2007-02-08 22:26:46 as along with 4 people and 2 groups pavanghatty karbak marcius papatonyhill BioinfoCIPF SGU-CIPF
	Structural biology: Molecular machinery in action [My Copy] Nature (21 January 2007) by Ad Bax, Dennis A. Torchia posted to protein_structure nmr by hmk on 2007-02-07 23:03:24 as
	An atomic environment potential for use in protein structure prediction. [My Copy] J Mol Biol, Vol. 352, No. 4. (30 September 2005), pp. 986-1001. by C. M. Summa, M. Levitt, W. F. Degrado posted to protein_structure decoy by hmk on 2007-01-30 23:11:31 as
	Meanfield approach to the thermodynamics of protein-solvent systems with application to p53. [My Copy] Biophysics, Vol. 80 (March 2001), pp. 1524-1537. by Volkel R. Armin, Noolandi Jaan posted to protein_structure graphical_models by hmk on 2007-01-29 19:24:03 as

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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

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