sebk's library 121 articles Export

	On the Accuracy of Homology Modeling and Sequence Alignment Methods Applied to Membrane Proteins [My Copy] Biophysical Journal, Vol. 91, No. 2. (15 July 2006), pp. 508-517. by L. Forrest, C. Tang, B. Honig posted to substitution structure sequence protein modelling membrane database alignment by sebk on 2009-11-17 16:44:17 as
	SCORE: predicting the core of protein models [My Copy] Bioinformatics, Vol. 17, No. 6. (1 June 2001), pp. 541-550. by Charlotte M. Deane, Quentin Kaas, Tom L. Blundell posted to structure protein modelling by sebk on 2009-09-11 20:41:39 as along with 2 people medic0747 cdeane
	Evolutionary potentials: structure specific knowledge-based potentials exploiting the evolutionary record of sequence homologs [My Copy] Genome Biology, Vol. 9, No. 4. (08 April 2008), R68. by Alejandro Panjkovich, Francisco Melo, Marc M. Renom posted to alignment modelling mqap protein sequence structure by sebk on 2009-08-07 16:02:43 as along with 2 people and 1 group kgutwin j3xucite KeatingJClub
	Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (12 December 2008), 531. by Shashi Pandit, Jeffrey Skolnick posted to alignment protein structure by sebk on 2009-08-07 16:00:12 as along with 3 people tny biehl reyez
	Advances and pitfalls of protein structural alignment. [My Copy] Current opinion in structural biology, Vol. 19, No. 3. (27 June 2009), pp. 341-348. by Hitomi Hasegawa, Liisa Holm posted to alignment protein review structure by sebk on 2009-08-07 15:58:46 as along with 4 people and 3 groups davidalee dgront sobolevnrm barry OPIG Orengo Group Journal Picks structural_bioinformatics
	QMEAN server for protein model quality estimation [My Copy] Nucl. Acids Res., Vol. 37, No. suppl_2. (1 July 2009), pp. W510-514. by Pascal Benkert, Michael Kunzli, Torsten Schwede posted to modelling mqap protein structure by sebk on 2009-07-21 13:24:38 as along with 3 people subramani sjcockell cat_hutchinson68
	Structural and functional restraints in the evolution of protein families and superfamilies. [My Copy] Biochemical Society transactions, Vol. 37, No. Pt 4. (August 2009), pp. 727-733. by S. Gong, C. L. Worth, G. R. Bickerton, S. Lee, D. Tanramluk, T. L. Blundell posted to environment-specific function protein sequence structure substitution by sebk on 2009-07-21 13:16:00 as along with 1 person and 1 group subramani OPIG
	Benchmarking consensus model quality assessment for protein fold recognition [My Copy] BMC Bioinformatics, Vol. 8, No. 1. (18 September 2007), 345. by Liam Mcguffin posted to modelling mqap protein structure by sebk on 2009-07-20 12:39:47 as along with 1 person massivemayhem
	A set of van der Waals and coulombic radii of protein atoms for molecular and solvent-accessible surface calculation, packing evaluation, and docking [My Copy] Proteins: Structure, Function, and Genetics, Vol. 32, No. 1. (1998), pp. 111-127. by Ai-Jun Li, Ruth Nussinov posted to modelling protein structure by sebk on 2009-07-14 19:06:33 as along with 1 person melo_mcr
	The packing density in proteins: standard radii and volumes1 [My Copy] Journal of Molecular Biology, Vol. 290, No. 1. (02 July 1999), pp. 253-266. by Jerry Tsai, Robin Taylor, Cyrus Chothia, Mark Gerstein posted to modelling protein structure by sebk on 2009-07-14 19:00:39 as along with 6 people and 3 groups ana barry bicko blackbart medic0747 sobolevnrm structural_bioinformatics Bioinformatics baker-group
	Excluded volume in protein side-chain packing [My Copy] Journal of Molecular Biology, Vol. 311, No. 1. (03 August 2001), pp. 183-193. by E. Kussell posted to modelling molecular_dynamics montecarlo protein sidechains structure by sebk on 2009-07-14 18:56:56 as along with 2 people and 2 groups ana carlk structural_bioinformatics Bioinformatics
	Fast procedure for reconstruction of full-atom protein models from reduced representations. [My Copy] Journal of computational chemistry, Vol. 29, No. 9. (15 July 2008), pp. 1460-1465. by Piotr Rotkiewicz, Jeffrey Skolnick posted to modelling protein structure by sebk on 2009-07-14 18:37:44 as along with 5 people Gabriel439 apaydin rsantana mijam middledomain
	Transmembrane protein topology prediction using support vector machines [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 159. by Timothy Nugent, David Jones posted to folding machine_learning membrane membrane-insertion protein sequence by sebk on 2009-07-08 13:17:12 as along with 3 people chocolate2009 TRHvidsten erexhepa
	Prediction of membrane-protein topology from first principles [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 20. (20 May 2008), pp. 7177-7181. by Andreas Bernsel, Håkan Viklund, Jenny Falk, Erik Lindahl, Gunnar von Heijne, Arne Elofsson posted to membrane membrane-insertion protein sequence structure by sebk on 2009-07-08 12:59:50 as along with 3 people and 2 groups druvus superpyrin sobolevnrm OPIG baker-group
	Molecular code for transmembrane-helix recognition by the Sec61 translocon. [My Copy] Nature, Vol. 450, No. 7172. (13 December 2007), pp. 1026-1030. by T. Hessa, N. M. Meindl-Beinker, A. Bernsel, et al.H. Kim, Y. Sato, M. Lerch-Bader, I. Nilsson, S. H. White, G. von Heijne posted to folding membrane membrane-insertion protein structure wet_lab by sebk on 2009-07-08 12:57:38 as
	Recognition of transmembrane helices by the endoplasmic reticulum translocon. [My Copy] Nature, Vol. 433, No. 7024. (27 January 2005), pp. 377-381. by T. Hessa, H. Kim, K. Bihlmaier, et al.C. Lundin, J. Boekel, H. Andersson, I. Nilsson, S. H. White, G. von Heijne posted to folding membrane membrane-insertion protein structure wet_lab by sebk on 2009-07-08 12:53:42 as along with 1 person ashaytan
	iMembrane: Homology-Based Membrane-Insertion of Proteins. [My Copy] Bioinformatics (Oxford, England) (23 February 2009) by Sebastian Kelm, Jiye Shi, Charlotte M. Deane posted to database environment-specific membrane membrane-insertion modelling molecular_dynamics protein sequence structure by sebk on 2009-06-23 19:53:17 as along with 2 people and 2 groups friendpine oteri OPIG Structural Biology Group TorVergata
	An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction [My Copy] Journal of Molecular Biology, Vol. 275, No. 5. (6 February 1998), pp. 895-916. by Ram Samudrala, John Moult posted to modelling mqap protein structure by sebk on 2009-06-23 19:49:32 as along with 1 person j3xucite
	High-resolution multi-dimensional NMR spectroscopy of proteins in human cells [My Copy] Nature, Vol. 458, No. 7234. (5 March 2009), pp. 106-109. by Kohsuke Inomata, Ayako Ohno, Hidehito Tochio, et al.Shin Isogai, Takeshi Tenno, Ikuhiko Nakase, Toshihide Takeuchi, Shiroh Futaki, Yutaka Ito, Hidekazu Hiroaki, Masahiro Shirakawa posted to protein structure wet_lab by sebk on 2009-04-15 18:46:54 as along with 5 people flbarroso cactus neils alexknight absterga
	Protein structure determination in living cells by in-cell NMR spectroscopy [My Copy] Nature, Vol. 458, No. 7234. (5 March 2009), pp. 102-105. by Daisuke Sakakibara, Atsuko Sasaki, Teppei Ikeya, et al.Junpei Hamatsu, Tomomi Hanashima, Masaki Mishima, Masatoshi Yoshimasu, Nobuhiro Hayashi, Tsutomu Mikawa, Markus Walchli, Brian O. Smith, Masahiro Shirakawa, Peter Guntert, Yutaka Ito posted to protein structure wet_lab by sebk on 2009-04-15 18:46:02 as along with 9 people and 1 group flbarroso eallain cactus barry cychen_cite ts3435 neils alexknight absterga McCammon
	Improving the quality of protein structure models by selecting from alignment alternatives [My Copy] BMC Bioinformatics, Vol. 7 (27 July 2006), 364. by Ingolf Sommer, Stefano Toppo, Oliver Sander, Thomas Lengauer, Silvio C. E. Tosatto posted to alignment machine_learning modelling mqap protein sequence structure by sebk on 2009-04-04 00:41:22 as along with 1 person newton1234
	Discarding Functional Residues from the Substitution Table Improves Predictions of Active Sites within Three-Dimensional Structures [My Copy] PLoS Comput Biol, Vol. 4, No. 10. (3 October 2008), e1000179. by Sungsam Gong, Tom L. Blundell posted to environment-specific function protein sequence structure substitution by sebk on 2009-03-25 12:11:04 as along with 7 people ssgong gjuggler joseph_x_zhou zwang bicko massivemayhem reyez
	The prediction of membrane protein structure and genome structural annotation. [My Copy] Comparative and functional genomics, Vol. 4, No. 4. (2003), pp. 406-409. by P. L. Martelli, P. Fariselli, G. Tasco, R. Casadio posted to machine_learning membrane membrane-insertion modelling protein sequence structure by sebk on 2009-02-13 15:09:52 as
	Prediction of helix-helix contacts and interacting helices in polytopic membrane proteins using neural networks [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 74, No. 4. (2009), pp. 857-871. by Angelika Fuchs, Andreas Kirschner, Dmitrij Frishman posted to helix-packing machine_learning membrane protein sequence structure by sebk on 2009-02-13 15:08:37 as along with 2 people dfdong middledomain
	Inter-residue interactions in protein structures exhibit power-law behavior. [My Copy] Biopolymers, Vol. 89, No. 12. (December 2008), pp. 1174-1178. by J. Gao, Z. Li posted to alignment membrane protein sequence structure by sebk on 2009-02-13 15:06:38 as
	Prediction of protein structural classes by Chou's pseudo amino acid composition: approached using continuous wavelet transform and principal component analysis. [My Copy] Amino acids (23 August 2008) by Zhan-Chao C. Li, Xi-Bin B. Zhou, Zong Dai, Xiao-Yong Y. Zou posted to alignment membrane protein sequence structure by sebk on 2009-02-13 15:04:19 as
	alpha-Helical Topology Prediction and Generation of Distance Restraints in Membrane Proteins [My Copy] Biophys. J., Vol. 95, No. 11. (1 December 2008), pp. 5281-5295. by Scott R. Mcallister, Christodoulos A. Floudas posted to helix-packing membrane modelling protein structure by sebk on 2009-02-13 15:01:38 as along with 1 person agrossfield
	A dual-scale approach toward structure prediction of retinal proteins. [My Copy] Journal of structural biology, Vol. 165, No. 1. (January 2009), pp. 37-46. by C. C. Chen, C. M. Chen posted to folding membrane membrane-insertion modelling molecular_dynamics montecarlo protein structure by sebk on 2009-02-13 15:00:18 as
	Sampling efficiency in explicit and implicit membrane environments studied by peptide folding simulations. [My Copy] Proteins (17 September 2008) by Jakob P P. Ulmschneider, Martin B B. Ulmschneider posted to folding membrane membrane-insertion modelling molecular_dynamics protein structure by sebk on 2009-02-13 14:59:19 as
	Comparative analysis of the packing topology of structurally important residues in helical membrane and soluble proteins [My Copy] Protein Engineering, Design and Selection (2 December 2008), gzn074. by Vagmita Pabuwal, Zhijun Li posted to helix-packing membrane protein structure by sebk on 2009-02-13 14:56:50 as along with 2 people carlosjavierna viktor21614
	A unified hydrophobicity scale for multispan membrane proteins [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA. by Julia Koehler, Nils Woetzel, René Staritzbichler, Charles R. Sanders, Jens Meiler posted to alignment membrane protein sequence substitution by sebk on 2009-02-13 14:55:57 as along with 2 people RamuAnandakrishnan paulschlesinger
	Detecting remote homologues using scoring matrices calculated from the estimation of amino acid substitution rates of beta-barrel membrane proteins. [My Copy] Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference, Vol. 1 (2008), pp. 1347-1350. by D. Jimenez-Morales, L. Adamian, J. Liang posted to alignment membrane protein sequence substitution by sebk on 2009-02-13 14:51:22 as
	Blind test of physics-based prediction of protein structures. [My Copy] Biophysical journal, Vol. 96, No. 3. (February 2009), pp. 917-924. by M. S. Shell, S. B. Ozkan, V. Voelz, G. A. Wu, K. A. Dill posted to folding modelling molecular_dynamics protein structure by sebk on 2009-02-13 14:50:08 as along with 1 person viktor21614
	Prediction of membrane protein structures with complex topologies using limited constraints [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 5. (3 February 2009), pp. 1409-1414. by P. Barth, B. Wallner, D. Baker posted to folding helix-packing membrane modelling protein structure by sebk on 2009-02-13 14:48:38 as along with 10 people and 2 groups rph dgront barry krapnik viktor21614 paulschlesinger zwang apaydin agrossfield amishp OPIG structural_bioinformatics
	SWISS-MODEL: An automated protein homology-modeling server. [My Copy] Nucleic Acids Res, Vol. 31, No. 13. (1 July 2003), pp. 3381-3385. by T. Schwede, J. Kopp, N. Guex, M. C. Peitsch posted to modelling protein structure by sebk on 2008-11-19 16:22:55 as along with 8 people flbarroso shacko bpb ffranca dgront gelack Haggan granujilla
	Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM. [My Copy] Proteins, Vol. Suppl 5 (2001), pp. 39-46. by P. A. Bates, L. A. Kelley, R. M. MacCallum, M. J. Sternberg posted to modelling protein structure by sebk on 2008-11-19 16:21:51 as along with 1 person Haggan
	Knowledge based modelling of homologous proteins, Part I: Three-dimensional frameworks derived from the simultaneous superposition of multiple structures. [My Copy] Protein Eng, Vol. 1, No. 5. (v 1987), pp. 377-384. by M. J. Sutcliffe, I. Haneef, D. Carney, T. L. Blundell posted to modelling protein structure by sebk on 2008-11-19 16:20:29 as along with 3 people and 2 groups ana warlock6x3 medic0747 structural_bioinformatics Bioinformatics
	Protein docking for low-resolution structures [My Copy] Protein Eng., Vol. 8, No. 4. (1 April 1995), pp. 371-378. by Ilya A. Vakser posted to docking protein structure by sebk on 2008-11-18 21:27:00 as
	Database resources of the National Center for Biotechnology Information [My Copy] Nucl. Acids Res., Vol. 37, No. Database issue. (21 October 2008), gkn741. by Eric W. Sayers, Tanya Barrett, Dennis A. Benson, et al.Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Ron Edgar, Scott Federhen, Michael Feolo, Lewis Y. Geer, Wolfgang Helmberg, Yuri Kapustin, David Landsman, David J. Lipman, Thomas L. Madden, Donna R. Maglott, Vadim Miller, Ilene Mizrachi, James Ostell, Kim D. Pruitt, Gregory D. Schuler, Edwin Sequeira, Stephen T. Sherry, Martin Shumway, Karl Sirotkin, Alexandre Souvorov, Grigory Starchenko, Tatiana A. Tatusova, Lukas Wagner, Eugene Yaschenko, Jian Ye posted to database protein sequence by sebk on 2008-11-18 21:11:27 as along with 6 people and 1 group vprieto daforerog robert85 Cortel lptolik reyez References for 3DSim paper
	Improved prediction of signal peptides: SignalP 3.0. [My Copy] Journal of molecular biology, Vol. 340, No. 4. (16 July 2004), pp. 783-795. by Jannick Dyrløv D. Bendtsen, Henrik Nielsen, Gunnar von Heijne, Søren Brunak posted to modelling protein sequence by sebk on 2008-11-18 20:57:25 as along with 10 people BioNica azazello tfuji rpetrenko katholt nedwards kreibich niallhaslam richter80 raiyar
	Membrane Proteins: From Sequence to Structure [My Copy] Annual Review of Biophysics and Biomolecular Structure, Vol. 23, No. 1. (1994), pp. 167-192. by G. V. Heijne posted to membrane modelling protein sequence structure by sebk on 2008-11-18 20:53:17 as
	The distribution of positively charged residues in bacterial inner membrane proteins correlates with the trans-membrane topology. [My Copy] The EMBO journal, Vol. 5, No. 11. (November 1986), pp. 3021-3027. by Gunnar von V. Heijne posted to membrane membrane-insertion protein structure by sebk on 2008-11-18 20:50:51 as
	Structural Prediction of Membrane-Bound Proteins [My Copy] European Journal of Biochemistry, Vol. 128, No. 2-3. (1982), pp. 565-575. by Patrick Argos, Mohana J. K. Rao, Paul A. Hargrave posted to membrane membrane-insertion modelling protein sequence structure by sebk on 2008-11-18 20:48:12 as
	Application of molecular dynamics with interproton distance restraints to three-dimensional protein structure determination. A model study of crambin. [My Copy] Journal of molecular biology, Vol. 191, No. 3. (5 October 1986), pp. 523-551. by G. M. Clore, A. T. Brünger, M. Karplus, A. M. Gronenborn posted to modelling molecular_dynamics protein structure by sebk on 2008-11-18 20:20:04 as along with 1 person kumar_physics
	MaxSub: an automated measure for the assessment of protein structure prediction quality. [My Copy] Bioinformatics, Vol. 16, No. 9. (September 2000), pp. 776-785. by N. Siew, A. Elofsson, L. Rychlewski, D. Fischer posted to mqap protein structure by sebk on 2008-11-18 20:11:52 as along with 6 people and 2 groups rabio granujilla BragilMassoud marcius dgront biehl BioinfoCIPF SGU-CIPF
	Unit-vector RMS (URMS) as a tool to analyze molecular dynamics trajectories. [My Copy] Proteins, Vol. 37, No. 4. (1 December 1999), pp. 554-564. by K. Kedem, L. P. Chew, R. Elber posted to alignment protein structure by sebk on 2008-11-18 20:10:23 as along with 2 people Lombardo_7 nigham
	Fast detection of common geometric substructure in proteins. [My Copy] Journal of computational biology : a journal of computational molecular cell biology, Vol. 6, No. 3-4. (r 1999), pp. 313-325. by L. P. Chew, D. Huttenlocher, K. Kedem, J. Kleinberg posted to alignment protein structure by sebk on 2008-11-18 20:08:44 as
	Comprehensive study on iterative algorithms of multiple sequence alignment [My Copy] Comput. Appl. Biosci., Vol. 11, No. 1. (1 February 1995), pp. 13-18. by Makoto Hirosawa, Yasushi Totoki, Masaki Hoshida, Masato Ishikawa posted to alignment protein sequence by sebk on 2008-11-18 20:05:50 as
	Amino acid substitution matrices from protein blocks. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 89, No. 22. (15 November 1992), pp. 10915-10919. by S. Henikoff, J. G. Henikoff posted to alignment protein sequence substitution by sebk on 2008-11-18 19:55:11 as along with 14 people rshe rpetrenko BioNica maria_hauser cmura alefox j3xucite cen4ik kaarsinogen dgront gurkanbebek Iden-J_GluR cjeans ashwinma
	GROMACS: fast, flexible, and free. [My Copy] Journal of computational chemistry, Vol. 26, No. 16. (December 2005), pp. 1701-1718. by D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark, H. J. Berendsen posted to modelling molecular_dynamics protein structure by sebk on 2008-11-18 19:48:28 as along with 20 people and 2 groups arifor krapnik r2s2 janneb dsmueller oteri choonpeng dimka jwm ttjoseph bilab rabio Dinler tji softsimu ashaytan robertvacha sunnytov Diego_Prada A_Coletta_Thesis Radiation_Damage Stressosome

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protein	113
structure	85
sequence	48
membrane	45
modelling	43
alignment	36
membrane-insertion	27
database	12
substitution	11
environment-specific	9
folding	9
molecular_dynamics	8
wet_lab	8
helix-packing	7
mqap	7
function	5
machine_learning	5
drug_design	4
review	4
docking	3
high_throughput_screening	3
interface	3
montecarlo	3
refinement	3
mutagenesis	1
networks	1
representation	1
sidechains	1

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