hmk's library 105 articles Export

	Recent Developments in Fragment-Based Drug Discovery [My Copy] Journal of Medicinal Chemistry, Vol. 51, No. 13. (1 July 2008), pp. 3661-3680. by Miles Congreve, Gianni Chessari, Dominic Tisi, Andrew J. Woodhead posted to review ligand_binding library drug_discovery drug_design by hmk on 2009-10-30 18:46:15 as along with 5 people and 1 group ubcg08l jerome higueruelo vaibhavdixit4 pslee Fragment Based Drug Discovery
	Coordinated amino acid changes in homologous protein families [My Copy] Protein Eng., Vol. 2, No. 3. (1 September 1988), pp. 193-199. by D. Altschuh, T. Vernet, P. Berti, D. Moras, K. Nagai posted to no-tag by hmk on 2009-10-06 08:49:49 as
	A multivariate von mises distribution with applications to bioinformatics [My Copy] Canadian Journal of Statistics, Vol. 36, No. 1. (2008), pp. 99-109. by Kanti V. Mardia, Gareth Hughes, Charles C. Taylor, Harshinder Singh posted to continuous_model by hmk on 2009-09-25 21:45:45 as
	Structural insight into the autoinhibition mechanism of AMP-activated protein kinase : Article : Nature [My Copy] posted to allostery camp by hmk on 2009-05-27 22:33:38 as
	Marginal MAP estimation using Markov chain Monte Carlo [My Copy] In ICASSP '99: Proceedings of the Acoustics, Speech, and Signal Processing, 1999. on 1999 IEEE International Conference (1999), pp. 1753-1756. by C. P. Robert, A. Doucet, S. J. Godsill posted to inference marginal_map by hmk on 2009-02-11 21:43:08 as
	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 5 people rabio kentsis apaydin nurban amishp
	$My PDF j&\#228;rvelin_00_ir.pdf$ IR evaluation methods for retrieving highly relevant documents [My Copy] In SIGIR '00: Proceedings of the 23rd annual international ACM SIGIR conference on Research and development in information retrieval (2000), pp. 41-48. by Kalervo J&\#228;rvelin, Jaana Kek&\#228;l&\#228;inen posted to no-tag by hmk on 2009-01-26 21:20:17 as along with 8 people and 1 group abellogin dekrays indratmo macle dvallet florianleitner pprett ldietz NETS-UAM
	HIV-1 Population Genetics and Adaptation in Newly Infected Individuals. [My Copy] Journal of virology (30 December 2008) by M Kearney, F Maldarelli, W Shao, et al.J B B. Margolick, E S S. Daar, J W W. Mellors, V Rao, J M M. Coffin, S Palmer posted to genetics hivprdata by hmk on 2009-01-17 22:07:37 as along with 2 people and 1 group wsjames mishar Oxford Virology
	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
	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
	Conditional random fields: Probabilistic models for segmenting and labeling sequence data [My Copy] (2001), pp. 282-289. by John Lafferty, Fernando Pereira posted to crf by hmk on 2009-01-06 13:45:07 as along with 1 person arafalov
	Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. [My Copy] Journal of molecular biology, Vol. 193, No. 4. (20 February 1987), pp. 775-791. by J. W. Ponder, F. M. Richards posted to rotamer_library side_chain_prediction by hmk on 2009-01-03 08:24:50 as
	Analysis of the relationship between side-chain conformation and secondary structure in globular proteins. [My Copy] J Mol Biol, Vol. 198, No. 2. (20 November 1987), pp. 295-310. by M. J. McGregor, S. A. Islam, M. J. Sternberg posted to rotamer_library side_chain_prediction by hmk on 2009-01-03 08:23:24 as along with 1 person allmensch
	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-François 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 15 people 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
	Lectures on Probability, Entropy, and Statistical Physics [My Copy] (31 Jul 2008) by Ariel Caticha posted to entropy jaynes physics probability statistics by hmk on 2008-09-18 06:15:43 as along with 12 people egcavalcanti janpaniev makni pdlug gniebler travieso petr cager ansobol jjray Borelli sbarthelme
	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
	On Sequential Monte Carlo Sampling Methods for Bayesian Filtering [My Copy] Statistics and Computing, Vol. 10 (2000), pp. 197-208. by Arnaud Doucet, Simon Godsill, Christophe Andrieu posted to inference marginal_map mcmc sampling statistics by hmk on 2008-09-12 17:57:39 as along with 2 people fierykylin ben500
	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
	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
	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
	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
	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 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 4 people and 2 groups 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
	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] Biophys. J., Vol. 93, No. 10. (15 November 2007), pp. 3460-3469. by Kei Moritsugu, Jeremy C. Smith posted to alternatives graphical_models molecular_dynamics protein_folding by hmk on 2007-12-09 03:09:17 as along with 3 people and 1 group 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
	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
	Information Theory and Statistical Mechanics [My Copy] Physical Review Online Archive (Prola), Vol. 106, No. 4. (15 May 1957), pp. 620-630. by E. T. Jaynes posted to inference information_theory molecular_mechanics statistics by hmk on 2007-12-07 06:41:06 as along with 11 people tictacgo vtraag Gorzomagnificent gokopal GomezAddams christoph_study ddahlem nathanielvirgo jenda_z varung dcoates
	Single-Molecule Dynamics Reveals Cooperative Binding-Folding in Protein Recognition [My Copy] PLoS Computational Biology, Vol. 2, No. 7. (1 July 2006), e78. by Jin Wang, Qiang Lu, Peter H. Lu posted to dynamics molecular_dynamics by hmk on 2007-12-07 03:51:09 as along with 1 person imthaone616

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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

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