mijam's library 185 articles Export

	Understanding Protein Evolution: From Protein Physics to Darwinian Selection [My Copy] Annual Review of Physical Chemistry, Vol. 59, No. 1. (2008), pp. 105-127. by Konstantin B. Zeldovich, Eugene I. Shakhnovich posted to protein_evolution modeling lattice by mijam on 2009-11-08 11:00:55 as along with 1 person flbarroso
	Protein Structure Prediction Using Rosetta [My Copy] Methods Enzymol In Numerical Computer Methods, Part D, Vol. 383 (2004), pp. 66-93. by C. Rohl, C. Strauss, K. Misura, D. Baker posted to loop by mijam on 2009-10-08 11:10:52 as along with 7 people granujilla bullli502 nigham thaliana dgront JimmyMac saunders
	Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field [My Copy] BMC Structural Biology, Vol. 7, No. 1. (29 June 2007), 43. by Sebastian Kmiecik, Dominik Gront, Andrzej Kolinski posted to loop by mijam on 2009-10-08 11:02:37 as along with 3 people wouterboomsma rabio sekmi
	The interplay of fold recognition and experimental structure determination in structural genomics [My Copy] Current Opinion in Structural Biology, Vol. 14, No. 3. (June 2004), pp. 307-312. by I. Friedberg posted to loop by mijam on 2009-10-08 11:00:14 as
	Inferring ideal amino acid interaction forms from statistical protein contact potentials. [My Copy] Proteins, Vol. 59, No. 1. (1 April 2005), pp. 49-57. by P. Pokarowski, A. Kloczkowski, R. L. Jernigan, N. S. Kothari, M. Pokarowska, A. Kolinski posted to loop by mijam on 2009-10-08 10:55:34 as along with 3 people RamuAnandakrishnan krapnik kgutwin
	SuperLooper--a prediction server for the modeling of loops in globular and membrane proteins. [My Copy] Nucleic acids research (8 May 2009) by Peter W W. Hildebrand, Andrean Goede, Raphael A A. Bauer, et al.Bjoern Gruening, Jochen Ismer, Elke Michalsky, Robert Preissner posted to loop by mijam on 2009-10-08 01:06:22 as along with 2 people viktor21614 reyez
	ArchDB: automated protein loop classification as a tool for structural genomics. [My Copy] Nucleic Acids Res, Vol. 32, No. Database issue. (1 January 2004) by J. Espadaler, N. Fernandez-Fuentes, A. Hermoso, et al.E. Querol, F. X. Aviles, M. J. Sternberg, B. Oliva posted to loop by mijam on 2009-10-08 01:05:57 as along with 2 people vavi baldo
	ArchPRED: a template based loop structure prediction server. [My Copy] Nucleic Acids Res, Vol. 34, No. Web Server issue. (1 July 2006) by N. Fernandez-Fuentes, J. Zhai, A. Fiser posted to loop by mijam on 2009-10-08 01:05:32 as along with 3 people vavi eckart_bindewald cdeane
	Modeling protein loops with knowledge-based prediction of sequence-structure alignment. [My Copy] Bioinformatics, Vol. 23, No. 21. (1 November 2007), pp. 2836-2842. by H. P. Peng, A. S. Yang posted to loop by mijam on 2009-10-08 01:04:57 as along with 2 people carlosjavierna cdeane
	Loop modeling: sampling, filtering, and scoring. [My Copy] Proteins (29 August 2007) by Cinque S S. Soto, Marc Fasnacht, Jiang Zhu, Lucy Forrest, Barry Honig posted to loop by mijam on 2009-10-08 01:02:54 as along with 2 people and 1 group granujilla cdeane OPIG
	LOOPER: a molecular mechanics-based algorithm for protein loop prediction [My Copy] Protein Engineering, Design and Selection (14 January 2008), gzm083. by Velin Z. Spassov, Paul K. Flook, Lisa Yan posted to loop by mijam on 2009-10-08 01:02:18 as
	Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. [My Copy] Nature methods, Vol. 6, No. 8. (August 2009), pp. 551-552. by Daniel J. Mandell, Evangelos A. Coutsias, Tanja Kortemme posted to loop by mijam on 2009-10-08 00:43:40 as along with 1 person tcschen
	Protein-Protein Docking with Backbone Flexibility [My Copy] Journal of Molecular Biology, Vol. 373, No. 2. (19 October 2007), pp. 503-519. by Chu Wang, Philip Bradley, David Baker posted to loop by mijam on 2009-10-08 00:36:34 as along with 6 people and 2 groups kgutwin csrocha barry jwm xdeupi Ema structural_bioinformatics Bioinformatics
	CREDO: A Protein-Ligand Interaction Database for Drug Discovery [My Copy] Chemical Biology & Drug Design, Vol. 73, No. 2. (February 2009), pp. 157-167. by Adrian Schreyer, Tom Blundell posted to ligands force_field docking by mijam on 2009-09-28 13:07:30 as along with 6 people richardbickerton pansapiens bicko nanonan massivemayhem higueruelo
	Bounds and Algorithms for Fast Exact Searches of Chemical Fingerprints in Linear and Sublinear Time [My Copy] Journal of Chemical Information and Modeling, Vol. 47, No. 2. (1 March 2007), pp. 302-317. by S. Joshua Swamidass, Pierre Baldi posted to fingerprints by mijam on 2009-09-24 20:59:21 as along with 2 people christoph_steinbeck baldigroup
	MMFF VII. Characterization of MMFF94, MMFF94s, and other widely available force fields for conformational energies and for intermolecular-interaction energies and geometries [My Copy] Journal of Computational Chemistry, Vol. 20, No. 7. (1999), pp. 730-748. by Thomas A. Halgren posted to force_field by mijam on 2009-09-24 18:28:30 as
	ROSETTALIGAND: Protein-small molecule docking with full side-chain flexibility [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 65, No. 3. (13 September 2006), pp. 538-548. by Jens Meiler, David Baker posted to vs by mijam on 2009-09-21 17:25:45 as along with 4 people and 1 group BragilMassoud kuhn jwm yongzhao TSRI_MGL
	Utility library for structural bioinformatics [My Copy] Bioinformatics, Vol. 24, No. 4. (15 February 2008), pp. 584-585. by Dominik Gront, Andrzej Kolinski posted to no-tag by mijam on 2009-06-30 16:05:44 as along with 5 people mcbla chad_davis dgront rabio Minty
	Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels. [My Copy] Proteins, Vol. 14, No. 2. (October 1992), pp. 309-323. by R. B. Russell, G. J. Barton posted to superimposition by mijam on 2009-06-30 11:53:10 as along with 3 people chad_davis analogAI jefferlyemerson
	Dopaminergic D1 and D2 Receptors Are Essential for the Arousal Effect of Modafinil [My Copy] J. Neurosci., Vol. 28, No. 34. (20 August 2008), pp. 8462-8469. by Wei-Min Qu, Zhi-Li Huang, Xin-Hong Xu, Naomi Matsumoto, Yoshihiro Urade posted to ampakines by mijam on 2009-06-19 10:54:33 as
	Dopamine D2High receptors stimulated by phencyclidines, lysergic acid diethylamide, salvinorin A, and modafinil. [My Copy] Synapse (New York, N.Y.), Vol. 63, No. 8. (August 2009), pp. 698-704. by P. Seeman, H. C. Guan, H. Hirbec posted to ampakines by mijam on 2009-06-19 10:50:58 as
	Calculation of protein backbone geometry from alpha-carbon coordinates based on peptide-group dipole alignment. [My Copy] Protein science : a publication of the Protein Society, Vol. 2, No. 10. (October 1993), pp. 1697-1714. by A. Liwo, M. R. Pincus, R. J. Wawak, S. Rackovsky, H. A. Scheraga posted to backbone by mijam on 2009-06-16 14:02:46 as
	Accurate modeling of protein conformation by automatic segment matching. [My Copy] J Mol Biol, Vol. 226, No. 2. (20 July 1992), pp. 507-533. by M. Levitt posted to backbone loop by mijam on 2009-06-16 13:44:04 as along with 4 people rabio warlock6x3 dgront granujilla
	Macromolecular Modeling with Rosetta [My Copy] Annual Review of Biochemistry, Vol. 77, No. 1. (2008), pp. 363-382. by Rhiju Das, David Baker posted to modeling rosetta by mijam on 2009-06-06 17:29:44 as along with 9 people bmduggan choonpeng kgutwin carlk phoenixzxl krapnik flbarroso saunders gisle
	Integrating Diverse Data for Structure Determination of Macromolecular Assemblies [My Copy] Annual Review of Biochemistry, Vol. 77, No. 1. (4 March 2008), pp. 443-477. by Frank Alber, Friedrich Förster, Dmitry Korkin, Maya Topf, Andrej Sali posted to cell_modeling by mijam on 2009-06-06 17:15:46 as along with 5 people kgutwin carlk noraziz chad_davis phoenixzxl
	Determining the architectures of macromolecular assemblies [My Copy] Nature, Vol. 450, No. 7170. (29 November 2007), pp. 683-694. by Frank Alber, Svetlana Dokudovskaya, Liesbeth M. Veenhoff, et al.Wenzhu Zhang, Julia Kipper, Damien Devos, Adisetyantari Suprapto, Orit Karni-Schmidt, Rosemary Williams, Brian T. Chait, Michael P. Rout, Andrej Sali posted to cell_modeling by mijam on 2009-06-06 16:47:48 as along with 9 people bicko chad_davis neils cjeans zwang CameronNeylon faion phoenixzxl higueruelo
	The molecular sociology of the cell [My Copy] Nature, Vol. 450, No. 7172. (12 December 2007), pp. 973-982. by Carol V. Robinson, Andrej Sali, Wolfgang Baumeister posted to cell_modeling by mijam on 2009-06-06 16:46:37 as along with 8 people guhjy cmmorel chad_davis grahamc cjeans phoenixzxl higueruelo megraw
	Protein structure prediction and structural genomics. [My Copy] Science, Vol. 294, No. 5540. (5 October 2001), pp. 93-96. by D. Baker, A. Sali posted to loop by mijam on 2009-06-05 16:16:36 as along with 11 people and 2 groups newton1234 saunders taikoo ana vavi dgront sriram_s mirzazadeh mingzhi granujilla janasont structural_bioinformatics Bioinformatics
	Hierarchical modeling of protein interactions [My Copy] Journal of Molecular Modeling, Vol. 13, No. 6. (1 July 2007), pp. 691-698. by Mateusz Kurcinski, Andrzej Kolinski posted to loop by mijam on 2009-06-04 18:41:29 as along with 3 people rabio mkurc naitsabes
	Characterization of protein-folding pathways by reduced-space modeling [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 30. (24 July 2007), pp. 12330-12335. by Sebastian Kmiecik, Andrzej Kolinski posted to loop by mijam on 2009-06-04 18:39:57 as along with 5 people carlosjavierna wouterboomsma mkurc sekmi nh
	Folding pathway of the B1 domain of protein G explored by a multiscale modeling [My Copy] Biophysical Journal, Vol. 94, No. 3. (21 September 2008), pp. 726-736. by Sebastian Kmiecik, Andrzej Kolinski posted to loop by mijam on 2009-06-04 18:38:46 as along with 2 people sekmi jennifermbui
	Protein fragment reconstruction using various modeling techniques. [My Copy] J Comput Aided Mol Des, Vol. 17, No. 11. (November 2003), pp. 725-738. by M. Boniecki, P. Rotkiewicz, J. Skolnick, A. Kolinski posted to loop by mijam on 2009-06-04 18:37:00 as along with 1 person dgront
	A "FRankenstein's monster" approach to comparative modeling: Merging the finest fragments of Fold-Recognition models and iterative model refinement aided by 3D structure evaluation [My Copy] Proteins: Structure, Function, and Genetics, Vol. 53, No. S6. (2003), pp. 369-379. by Jan Kosinski, Iwona A. Cymerman, Marcin Feder, Michal A. Kurowski, Joanna M. Sasin, Janusz M. Bujnicki posted to loop by mijam on 2009-06-04 18:35:46 as along with 2 people and 1 group Einat dgront structural_bioinformatics
	Critical assessment of methods of protein structure prediction-Round VII. [My Copy] Proteins, Vol. 69 Suppl 8, No. S8. (5 October 2007), pp. 3-9. by J. Moult, K. Fidelis, A. Kryshtafovych, B. Rost, T. Hubbard, A. Tramontano posted to loop by mijam on 2009-06-04 18:27:28 as along with 5 people timhubbard mcbla j3xucite nigham saunders
	Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models. [My Copy] Proteins, Vol. 61, No. Suppl 7. (26 September 2005), pp. 84-90. by Andrzej Kolinski, Janusz M. Bujnicki posted to loop by mijam on 2009-06-04 18:26:02 as along with 4 people and 2 groups mcbla nigham marcius dgront BioinfoCIPF SGU-CIPF
	Protein structure modeling with MODELLER. [My Copy] Methods in molecular biology (Clifton, N.J.), Vol. 426 (2008), pp. 145-159. by N. Eswar, D. Eramian, B. Webb, M. Y. Shen, A. Sali posted to loop by mijam on 2009-06-04 18:23:58 as
	Comparative modeling for protein structure prediction. [My Copy] Curr Opin Struct Biol (27 February 2006) by Krzysztof Ginalski posted to loop by mijam on 2009-06-04 18:21:30 as along with 8 people mcbla BragilMassoud kuhn rabio schuylrp ruvido insectopalo granujilla
	Comparison of three Monte Carlo conformational search strategies for a proteinlike homopolymer model: Folding thermodynamics and identification of low-energy structures [My Copy] The Journal of Chemical Physics, Vol. 113, No. 12. (2000), pp. 5065-5071. by Dominik Gront, Andrzej Kolinski, Jeffrey Skolnick posted to loop by mijam on 2009-06-04 17:46:52 as along with 3 people dgront sikorski rabio
	Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features [My Copy] Biopolymers, Vol. 22, No. 12. (December 1983), pp. 2577-2637. by W. Kabsch, C. Sander posted to loop by mijam on 2009-06-04 17:44:02 as along with 31 people Vadikus j3xucite scampos TLVincent maria_hauser pablocarb rpetrenko carlosjavierna wqia007 dsmueller niallhaslam saunders jwm sebk Diego_Prada pjcite kaarsinogen lna chad_davis wouterboomsma penka ffranca dgront choonpeng rabio gisle medic0747 martainn chgjb mschofie marti
	Modeling of loops in protein structures. [My Copy] Protein Sci, Vol. 9, No. 9. (September 2000), pp. 1753-1773. by A. Fiser, R. K. Do, A. Sali posted to loop by mijam on 2009-06-04 17:42:11 as along with 5 people warlock6x3 vavi ttjoseph mirzazadeh tji
	Some methods for classification and analysis of multivariate observations [My Copy] In Fifth Berkeley Symposium on Mathematical Statistics and Probability (1967), pp. 281-297. by J. Macqueen edited by University posted to kmeans by mijam on 2009-06-03 12:58:28 as along with 3 people Diego_Prada votis sugarexpletive
	Replica Monte Carlo Simulation of Spin-Glasses [My Copy] Physical Review Letters, Vol. 57, No. 21. (24 November 1986), 2607. by Robert H. Swendsen, Jian-Sheng Wang posted to loop mc by mijam on 2009-06-03 12:51:51 as along with 6 people Sylvain_Prigent dgront sikorski rabio qwermish iantunbridge
	A hierarchical approach to all-atom protein loop prediction. [My Copy] Proteins, Vol. 55, No. 2. (1 May 2004), pp. 351-367. by M. P. Jacobson, D. L. Pincus, C. S. Rapp, et al.T. J. Day, B. Honig, D. E. Shaw, R. A. Friesner posted to loop by mijam on 2009-06-03 12:06:56 as along with 4 people and 1 group vavi yongzhao sschurer allmensch TSRI_MGL
	Long loop prediction using the protein local optimization program. [My Copy] Proteins (22 August 2006) by Kai Zhu, David L L. Pincus, Suwen Zhao, Richard A A. Friesner posted to loop by mijam on 2009-06-03 12:01:08 as along with 2 people vavi cdeane
	Loopholes and missing links in protein modeling. [My Copy] Protein Sci, Vol. 16, No. 9. (September 2007), pp. 1999-2012. by K. A. Rossi, C. A. Weigelt, A. Nayeem, S. R. Krystek posted to loop by mijam on 2009-05-05 14:18:25 as along with 2 people cdeane LamBras
	Solvation free energies calculated using the GB/SA model: Sensitivity of results on charge sets, protocols, and force fields [My Copy] Journal of Computational Chemistry, Vol. 19, No. 7. (1998), pp. 769-780. by Rami M. Reddy, Mark D. Erion, Atul Agarwal, Vellarkad N. Viswanadhan, Quentin D. Mcdonald, Clark W. Still posted to asa hydrophobicity by mijam on 2009-04-25 21:26:38 as along with 1 person dfgreen
	Yerba Mate Tea (<i>Ilex paraguariensis</i>): A Comprehensive Review on Chemistry, Health Implications, and Technological Considerations [My Copy] Journal of Food Science, Vol. 72, No. 9. (2007), pp. R138-R151. by C. I. Heck, E. G. de Mejia posted to yerba by mijam on 2009-04-22 15:47:53 as
	Principal eigenvector of contact matrices and hydrophobicity profiles in proteins [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 58, No. 1. (2 November 2004), pp. 22-30. by Ugo Bastolla, Markus Porto, Eduardo H. Roman, Michele Vendruscolo posted to no-tag by mijam on 2009-04-22 12:16:30 as along with 1 person vavi
	Entropic Cost of Protein−Ligand Binding and Its Dependence on the Entropy in Solution [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Sheeba J. Irudayam, Richard H. Henchman posted to docking entropy by mijam on 2009-04-20 10:15:36 as along with 2 people and 1 group agrossfield sobolevnrm baker-group
	RMS/Coverage graphs: A qualitative method for comparing three-dimensional protein structure predictions [My Copy] Proteins: Structure, Function, and Genetics, Vol. 37, No. S3. (1999), pp. 15-21. by Tim J. P. Hubbard posted to no-tag by mijam on 2009-04-20 10:01:27 as along with 1 person rabio

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loop	36
asa	27
thesis	13
hydrophobicity	12
docking	11
potentials	10
statistical	10
dee	9
entropy	7
rotamer	7
ampakines	6
struct_alignment	5
protein_folding	4
cell_modeling	3
distance_geometry	3
h-bond	3
rosetta	3
vs	3
backbone	2
force_field	2
lcap	2
modeling	2
qm_mm	2
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contact	1
fingerprints	1
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homology_modeling	1
kmeans	1
lattice	1
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map	1
mc	1
md	1
modeller	1
protein_evolution	1
similarity	1
superimposition	1
xray	1
yerba	1

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