Tag structure_prediction [131 articles] Export

Recent papers classified by the tag structure_prediction.

	Accurate Automated Protein NMR Structure Determination Using Unassigned NOESY Data [My Copy] Journal of the American Chemical Society, Vol. 0, No. 0. (0000) by Srivatsan Raman, Yuanpeng J. Huang, Binchen Mao, et al.Paolo Rossi, James M. Aramini, Gaohua Liu, Gaetano T. Montelione, David Baker posted to structure_prediction structural_model rosetta protein-structure nmr dec09 chemical_shift by klexa on 2009-12-14 15:43:23 as
	PatchDock and SymmDock: servers for rigid and symmetric docking. [My Copy] Nucleic acids research, Vol. 33, No. Web Server issue. (1 July 2005) by Dina Schneidman-Duhovny, Yuval Inbar, Ruth Nussinov, Haim J. Wolfson posted to web_servers structure_prediction protein_interaction protein ace by csrocha to the group structural_bioinformatics on 2009-12-13 16:17:11 as along with 1 person bicko
	A composite score for predicting errors in protein structure models [My Copy] Protein Science, Vol. 15, No. 7. (July 2006), pp. 1653-1666. by David Eramian, Min-yi Shen, Damien Devos, Francisco Melo, Andrej Sali, Marc A. Marti-Renom posted to svm structure_prediction statistical_potentials fold_recognition comparative_modeling by rabio on 2009-11-27 10:58:46 as along with 5 people dimka vavi wouterboomsma mijam j3xucite
	Progress in structure prediction of α-helical membrane proteins [My Copy] Current Opinion in Structural Biology, Vol. 16, No. 4. (3 August 2006), pp. 496-504. by S. Fleishman, N. Bental posted to structure_prediction membrane_protein alpha-helices by viktor21614 on 2009-11-11 16:20:15 as along with 2 people and 1 group xdeupi wouterboomsma LabCompMed
	Computation of conformational coupling in allosteric proteins. [My Copy] PLoS computational biology, Vol. 5, No. 8. (28 August 2009), e1000484. by Brian A. Kidd, David Baker, Wendy E. Thomas posted to structure_prediction protein-ligand_interactions allostery by sobolevnrm on 2009-10-31 00:12:01 as along with 8 people and 1 group apaydin skywalkerus02 klexa oteri boris_aguilar bmduggan barry zwang McCammon
	HOW WELL CAN SIMULATION PREDICT PROTEIN FOLDING KINETICS AND THERMODYNAMICS? [My Copy] Annual Review of Biophysics and Biomolecular Structure, Vol. 34, No. 1. (29 October 2005), pp. 43-69. by Christopher D. Snow, Eric J. Sorin, Young M. Rhee, Vijay S. Pande posted to thermodynamics structure_prediction simulations proteins kinetics by amphibina on 2009-10-27 07:33:22 as along with 10 people krapnik flbarroso Diego_Prada doktornoe dgront blackbart allmensch saunders evanse toerst
	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 structure_prediction rosetta energy_function de_novo conformation_serching by rabio on 2009-10-12 10:09:19 as along with 6 people mijam kentsis apaydin nurban hmk amishp
	Progress in Modeling of Protein Structures and Interactions [My Copy] Science, Vol. 310, No. 5748. (28 October 2005), pp. 638-642. by Ora Schueler-Furman, Chu Wang, Phil Bradley, Kira Misura, David Baker posted to structure_prediction review by rabio on 2009-10-12 09:15:34 as along with 18 people and 3 groups krapnik ucbcjbm paddydu flbarroso thaliana jwm vavi bicko KyuhoLee marcius eweaver tny nickolay dgront rsantana mirzazadeh insectopalo barry BioinfoCIPF SGU-CIPF structural_bioinformatics
	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 structure_fragments structure_prediction by rabio on 2009-06-25 15:21:30 as along with 4 people mijam warlock6x3 dgront granujilla
	Modelling the polypeptide backbone with 'spare parts' from known protein structures [My Copy] Protein Eng., Vol. 2, No. 5. (1 January 1989), pp. 335-345. by Michel Claessens, Eric van Cutsem, Ignace Lasters, Shoshana Wodak posted to structure_fragments structure_prediction by rabio on 2009-06-25 15:20:21 as along with 2 people j3xucite dgront
	Predictions of RNA secondary structure by combining homologous sequence information [My Copy] Bioinformatics, Vol. 25, No. 12. (15 June 2009), pp. i330-338. by Michiaki Hamada, Kengo Sato, Hisanori Kiryu, Toutai Mituyama, Kiyoshi Asai posted to rna structure_prediction by AlexBateman to the group Journal picks on 2009-06-01 10:52:06 as along with 1 person mtagaya
	Increasing the precision of comparative models with YASARA NOVA - a self-parameterizing force field [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 47, No. 3. (2002), pp. 393-402. by Elmar Krieger, Günther Koraimann, Gert Vriend posted to molecular_simulation optimization structure_prediction by sobolevnrm to the group baker-group on 2009-04-23 12:29:22 as
	Statistical Theory of Protein Sequence Design by Random Mutation [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Arnab Bhattacherjee, Parbati Biswas posted to bioinformatics protein_engineering structure_prediction by sobolevnrm to the group baker-group on 2009-03-28 16:16:11 as
	Building alternate protein structures using the elastic network model [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA. by Qingyi Yang, Kim A. Sharp posted to enhanced_sampling quasiharmonic_models structure_prediction by sobolevnrm to the group baker-group on 2009-03-25 11:36:50 as along with 5 people and 1 group pansapiens klexa abovell oteri middledomain Structural Biology Group TorVergata
	Comparative analysis of coiled-coil prediction methods. [My Copy] Journal of structural biology, Vol. 155, No. 2. (August 2006), pp. 140-145. by Markus Gruber, Johannes Söding, Andrei N. Lupas posted to structure_prediction by oteri to the group Structural Biology Group TorVergata on 2008-12-31 11:43:15 as along with 5 people TLVincent kgutwin cjeans ca3295 marck
	MultiCoil: a program for predicting two- and three-stranded coiled coils. [My Copy] Protein science : a publication of the Protein Society, Vol. 6, No. 6. (June 1997), pp. 1179-1189. by E. Wolf, P. S. Kim, B. Berger posted to structure_prediction by oteri to the group Structural Biology Group TorVergata on 2008-12-31 10:34:34 as along with 3 people TLVincent kgutwin ca3295
	Paircoil2: improved prediction of coiled coils from sequence [My Copy] Bioinformatics, Vol. 22, No. 3. (1 February 2006), pp. 356-358. by A. V. McDonnell, T. Jiang, A. E. Keating, B. Berger posted to structure_prediction programmi coiled_coil by oteri on 2008-12-31 10:05:18 as along with 1 person and 1 group TLVincent Structural Biology Group TorVergata
	3D-Jury: a simple approach to improve protein structure predictions [My Copy] Bioinformatics, Vol. 19, No. 8. (22 May 2003), pp. 1015-1018. by K. Ginalski, A. Elofsson, D. Fischer, L. Rychlewski posted to comparative_modeling structure_prediction structure_similarity threading tools by rabio on 2008-11-05 14:27:14 as along with 6 people newton1234 mcbla karbak dgront schuylrp mijam
	Using inferred residue contacts to distinguish between correct and incorrect protein models. [My Copy] Bioinformatics (Oxford, England), Vol. 24, No. 14. (15 July 2008), pp. 1575-1582. by Christopher S. Miller, David Eisenberg posted to bayesian_inference model_discrimination structure_prediction by cmura to the group MuraLab on 2008-10-23 23:15:59 as along with 1 person dfdong
	Kemp elimination catalysts by computational enzyme design [My Copy] Nature, Vol. 453, No. 7192. (19 March 2008), pp. 190-195. by Daniela Rothlisberger, Olga Khersonsky, Andrew M. Wollacott, et al.Lin Jiang, Jason DeChancie, Jamie Betker, Jasmine L. Gallaher, Eric A. Althoff, Alexandre Zanghellini, Orly Dym, Shira Albeck, Kendall N. Houk, Dan S. Tawfik, David Baker posted to protein_engineering structure_prediction by sobolevnrm to the group baker-group on 2008-06-27 12:04:48 as along with 12 people and 2 groups barmak7282 baiaixi whitead qbin1304 fralium Diego_Prada apaydin jwm msuarezdiez austin cactus neils Jiang Research Group Biocatalysis and Biotransformation
	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 biomembranes protein-membrane_interactions structure_prediction by sobolevnrm to the group baker-group on 2008-05-20 20:09:19 as along with 3 people and 1 group sebk druvus superpyrin OPIG
	I-TASSER server for protein 3D structure prediction [My Copy] BMC Bioinformatics, Vol. 9 (23 January 2008), 40. by Yang Zhang posted to structure_prediction by rabio on 2008-04-14 19:28:05 as along with 5 people saunders chad_davis mkurc zwang mclarenv
	Monte Carlo refinement of rigid-body protein docking structures with backbone displacement and side-chain optimization. [My Copy] Protein science : a publication of the Protein Society, Vol. 16, No. 12. (1 December 2007), pp. 2716-2725. by Stephan Lorenzen, Yang Zhang posted to protein-protein_interactions structure_prediction by sobolevnrm to the group baker-group on 2007-12-21 12:26:27 as
	A correlation-based method for the enhancement of scoring functions on funnel-shaped energy landscapes [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 63, No. 1. (2006), pp. 155-164. by Andrew W. Stumpff-Kane, Michael Feig posted to protein-ligand_interactions structure_prediction by sobolevnrm to the group baker-group on 2007-12-18 13:05:12 as
	Prediction of the structure of symmetrical protein assemblies [My Copy] Proceedings of the National Academy of Sciences (31 October 2007), 0702626104. by Ingemar Andre, Philip Bradley, Chu Wang, David Baker posted to structure_prediction by sobolevnrm to the group baker-group on 2007-12-18 12:53:24 as along with 4 people and 1 group jwm jmrivort cjeans zwang Supramolecular
	High-resolution structure prediction and the crystallographic phase problem [My Copy] Nature, Vol. 450, No. 7167. (14 October 2007), pp. 259-264. by Bin Qian, Srivatsan Raman, Rhiju Das, et al.Philip Bradley, Airlie J. McCoy, Randy J. Read, David Baker posted to protein_folding structure_prediction by sobolevnrm to the group baker-group on 2007-12-17 12:41:21 as along with 16 people and 1 group bmduggan newton1234 apaydin aheilbut jwm eckart_bindewald ffranca dgront massivemayhem cjeans zwang cactus boris_aguilar Ema chenway ardalby OPIG
	Protein Structure Prediction in 1D, 2D, and 3D [My Copy] In The Encyclopaedia of Computational Chemistry, Vol. 3 (1998), pp. 2242-2255. by Burkhard Rost posted to structure_prediction by rabio on 2007-12-06 15:12:04 as
	Identifying sequence-structure pairs undetected by sequence alignments [My Copy] Protein Engineering, Vol. 13, No. 7. (1 July 2000), pp. 459-475. by Sanzo Miyazawa, Robert L. Jernigan posted to sequence_analysis structure_similarity structure_prediction by rabio on 2007-10-04 13:24:21 as along with 1 person krapnik
	Automated de novo prediction of native-like RNA tertiary structures [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 37. (11 September 2007), pp. 14664-14669. by Rhiju Das, David Baker posted to ab-initio rna structure_prediction by marcius on 2007-09-01 10:46:02 as along with 8 people and 2 groups fisherp rsaito jwm eckart_bindewald zwang physics Ema reyez BioinfoCIPF SGU-CIPF
	Predicting transmembrane protein topology with a hidden markov model: application to complete genomes1 [My Copy] Journal of Molecular Biology, Vol. 305, No. 3. (19 January 2001), pp. 567-580. by Anders Krogh, Björn Larsson, Gunnar von Heijne, Erik L. L. Sonnhammer posted to hidden_markov membrane_proteins structure_prediction by andreasauerwein on 2007-08-23 13:46:16 as along with 11 people azazello tfuji niallhaslam katholt thaliana bjorns j3xucite happy_manatee massivemayhem twenta sebk
	Comparative protein modelling by satisfaction of spatial restraints [My Copy] Journal of Molecular Biology, Vol. 234, No. 3. (5 December 1993), pp. 779-815. by A. Sali, T. L. Blundell posted to comparative_modeling restraints structure_prediction by rabio on 2007-07-19 15:19:05 as along with 17 people krapnik bmduggan pjcite newton1234 viktor21614 mijam dimka vavi bicko chad_davis ttjoseph skhadar dgront massivemayhem medic0747 sebk granujilla
	Monte Carlo simulation of proteins through a random walk in energy space [My Copy] The Journal of Chemical Physics, Vol. 116, No. 16. (2002), pp. 7225-7230. by Nitin Rathore, Juan J. de Pablo posted to histograms monte_carlo phase_transition protein_thermodynamics reduced_models sicho simualted_aniling wang-landau_sampling structure_prediction by rabio on 2007-02-27 13:55:13 as along with 1 person Paulius_m
	Sequence comparison and protein structure prediction [My Copy] Current Opinion in Structural Biology, Vol. 16, No. 3. (June 2006), pp. 374-384. by Roland L. Dunbrack posted to sequence_analysis review structure_prediction by rabio on 2007-02-02 17:27:08 as along with 6 people flbarroso agustinarce wouterboomsma xiaobeizhao schuylrp jwm
	COPS-Cis/trans peptide bond conformation prediction of amino acids on the basis of secondary structure information [My Copy] Bioinformatics, Vol. 21, No. 5. (01 March 2005), pp. 685-686. by Doreen Pahlke, Dietmar Leitner, Urs Wiedemann, Dirk Labudde posted to structure_prediction by rabio on 2006-12-29 12:36:50 as
	Prediction of Peptide Conformation by Multicanonical Algorithm: A New Approach to the Multiple-Minima Problem [My Copy] (25 January 1993) by Ulrich H. E. Hansmann, Yuko Okamoto posted to lattice_models monte_carlo multicanonical_ensemble structure_prediction by rabio on 2006-12-29 12:19:53 as
	Statistical thermodynamics of protein folding: Comparison of a mean-field theory with Monte Carlo simulations [My Copy] The Journal of Chemical Physics, Vol. 102, No. 3. (1995), pp. 1334-1348. by Ming H. Hao, Harold A. Scheraga posted to entropy_sampling force_field mean-field monte_carlo multicanonical_ensemble protein_folding protein_thermodynamics reduced_models review structure_prediction by rabio on 2006-12-11 14:36:54 as
	New Monte Carlo algorithms for protein folding [My Copy] Current Opinion in Structural Biology, Vol. 9, No. 2. (April 1999), pp. 177-183. by U. H. Hansmann, Y. Okamoto posted to monte_carlo protein_folding review structure_prediction by rabio on 2006-12-11 14:32:21 as along with 6 people apaydin flbarroso dgront insectopalo iantunbridge nigham
	Reduced models of proteins and their applications [My Copy] Polymer In Conformational Protein Conformations, Vol. 45, No. 2. (January 2004), pp. 511-524. by Andrzej Kolinski, Jeffrey Skolnick posted to cabs lattice_models monte_carlo reduced_models review rosetta sicho unres structure_prediction continuous_models by rabio on 2006-12-11 13:01:23 as along with 3 people mijam mcbla iantunbridge
	Generalized comparative modeling (GENECOMP): a combination of sequence comparison, threading, and lattice modeling for protein structure prediction and refinement. [My Copy] Proteins, Vol. 44, No. 2. (1 August 2001), pp. 133-149. by A. Kolinski, M. R. Betancourt, D. Kihara, P. Rotkiewicz, J. Skolnick posted to constraints homology_modeling knowledge-based_potentials replica_method threading structure_prediction by rabio on 2006-12-10 22:30:25 as along with 2 people mijam dgront
	Protein structure prediction by tempering spatial constraints [My Copy] Journal of Computer-Aided Molecular Design, Vol. 19, No. 8. (August 2005), pp. 603-608. by Dominik Gront, Andrzej Kolinski, Ulrich Hansmann posted to monte_carlo replica_method structure_prediction by rabio on 2006-12-10 22:24:04 as
	Protein modeling and structure prediction with a reduced representation [My Copy] Acta Biochimica Polonica, Vol. 51, No. 2. (2004), pp. 349-371. by A. Kolinski posted to cabs lattice_models tools structure_prediction by rabio on 2006-12-01 12:36:03 as along with 5 people vavi dgront sekmi mijam mcbla
	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 protein_structure structure_fragments structure_prediction by ana to the group structural_bioinformatics on 2006-11-03 22:45:52 as along with 12 people and 1 group chemrahul82 paddydu Diego_Prada reyez guxiyou jwm vavi wouterboomsma j3xucite hmk mijam joule Bioinformatics
	Protein decoy assembly using short fragments under geometric constraints. [My Copy] Biopolymers, Vol. 68, No. 3. (March 2003), pp. 278-285. by R. Kolodny, M. Levitt posted to modeling protein_structure structure_prediction by ana on 2006-10-31 22:45:00 as along with 1 person and 2 groups lgarreta structural_bioinformatics Bioinformatics
	Evolution and physics in comparative protein structure modeling. [My Copy] Acc Chem Res, Vol. 35, No. 6. (June 2002), pp. 413-421. by A. Fiser, M. Feig, C. L. Brooks, A. Sali posted to comparative_modeling structure_prediction by vavi on 2006-10-11 16:51:26 as along with 2 people and 2 groups barry insectopalo structural_bioinformatics Bioinformatics
	Toward High-Resolution de Novo Structure Prediction for Small Proteins [My Copy] Science, Vol. 309, No. 5742. (16 September 2005), pp. 1868-1871. by Philip Bradley, Kira M. S. Misura, David Baker posted to structure_prediction by gbart on 2006-10-04 16:34:01 as along with 11 people and 4 groups ucbcjbm paddydu kgutwin BragilMassoud ana barry thaliana jwm vavi marcius thamelry structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
	Computer modeling 16 S ribosomal RNA [My Copy] Journal of Molecular Biology, Vol. 221, No. 3. (5 October 1991), pp. 889-907. by John M. Hubbard, John E. Hearst posted to algorithms bioinformatics rna structure_prediction by marcius to the group SGU-CIPF on 2006-09-07 13:31:07 as along with 1 person and 1 group eckart_bindewald BioinfoCIPF
	CODA: a combined algorithm for predicting the structurally variable regions of protein models. [My Copy] Protein Sci, Vol. 10, No. 3. (March 2001), pp. 599-612. by C. M. Deane, T. L. Blundell posted to hybrid protein structure_prediction by vavi on 2006-08-05 13:07:33 as along with 2 people medic0747 cdeane
	Prediction of loop geometries using a generalized born model of solvation effects [My Copy] Proteins: Structure, Function, and Genetics, Vol. 35, No. 2. (1999), pp. 173-183. by Chaya S. Rapp, Richard A. Friesner posted to ab_initio molecular_dynamics monte_carlo protein structure_prediction by vavi on 2006-07-31 09:23:54 as
	Exploratory studies of ab initio protein structure prediction: multiple copy simulated annealing, AMBER energy functions, and a generalized born/solvent accessibility solvation model. [My Copy] Proteins, Vol. 46, No. 1. (1 January 2002), pp. 128-146. by Y. Liu, D. L. Beveridge posted to ab_initio molecular_dynamics monte_carlo protein simulated_annealing structure_prediction by vavi on 2006-07-31 09:00:25 as along with 1 person flbarroso
	Structural prediction of peptides bound to MHC class I. [My Copy] J Mol Biol, Vol. 356, No. 2. (17 February 2006), pp. 521-546. by T. Fagerberg, J. C. Cerottini, O. Michielin posted to molecular_dynamics protein simulated_annealing structure_prediction by vavi on 2006-07-31 08:54:09 as

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protein_structure	101
review	49
bioinformatics	47
statistical_potentials	43
comparative_modeling	40
casp	39
biophysics	36
computational_biology	36
cafasp	33
sequence_alignment	27
ab-initio	24
protein_sequence	18
rna	18
model_assessment	15
algorithms	13
contact_maps	10
protein	10
structure_comparison	10
membrane_protein	9
structural_genomics	9
structure_alignment	9
computational	8
monte_carlo	8
benchmark	6
evolution	6
protein_fragments	6
sequence_comparison	6
water-mediated_contacts	6
structure_fragments	5
threading	5
15872	4
ab_initio	4
loop_modeling	4
protein_engineering	4
protein_folding	4
rosetta	4
clustering	3
comparative_genomics	3
contact_map	3
databases	3
folding	3
homology_analogy	3
indels	3
lattice_models	3
microarray	3
model_evaluation	3
model_refinement	3
modeling	3
molecular_dynamics	3
multiple_structure_comparison	3
pca	3
protein-ligand_interactions	3
protein_evolution	3
protein_universe	3
pseudoknot	3
reduced_models	3
secondary_structure	3
sequence	3
sequence-structure	3
sequence_structure	3
servers	3
structure	3
structure_classification	3
structure_core	3
structure_flexible	3
ace	2
biomembranes	2
cabs	2
chemical_shift	2
dec09	2
enhanced_sampling	2
molecular_simulation	2
multicanonical_ensemble	2
ncrna	2
nmr	2
optimization	2
protein-membrane_interactions	2
protein-protein_interactions	2
protein-structure	2
protein_interaction	2
protein_thermodynamics	2
quasiharmonic_models	2
replica_method	2
sequence_analysis	2
sicho	2
simulated_annealing	2
structural_model	2
structure_similarity	2
tools	2
web_servers	2
allostery	1
de_novo	1
fold_recognition	1
fragment_approach	1
hybrid	1
kinetics	1
restraints	1
secondary_structure_prediction	1
simulations	1
svm	1

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