Tag comparative_modeling [75 articles] Export

Recent papers classified by the tag comparative_modeling.

	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
	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 by mcbla on 2009-04-30 22:52:56 as along with 6 people newton1234 rabio karbak dgront schuylrp mijam
	Amino acid substitution matrices from protein blocks. [My Copy] Proc Natl Acad Sci U S A, Vol. 89, No. 22. (15 November 1992), pp. 10915-10919. by S. Henikoff, J. G. Henikoff posted to comparative_modeling by mcbla on 2009-04-29 20:25:26 as along with 1 person gisle
	Where did the BLOSUM62 alignment score matrix come from? [My Copy] Nature Biotechnology, Vol. 22, No. 8. (August 2004), pp. 1035-1036. by Sean R. Eddy posted to comparative_modeling by mcbla on 2009-04-29 20:13:54 as along with 7 people and 1 group svozil ziquje bicko gurkanbebek xiaobeizhao rabio reyez Bioinformatics
	Identification of common molecular subsequences [My Copy] Journal of Molecular Biology, Vol. 147, No. 1. (25 March 1981), pp. 195-197. by T. F. Smith, M. S. Waterman posted to comparative_modeling by mcbla on 2009-04-29 19:34:46 as along with 21 people rshe jengeldk maria_hauser jmanning2k cmor parnell adamnellis timflutre heliopais alessandroparini usagi-kirin creswick vavi bicko dgront rabio cjeans incovoma sujaikumar newton1234 bozdagd
	Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models. [My Copy] Proteins, Vol. 61 Suppl 7 (26 September 2005), pp. 84-90. by Andrzej Koliński, Janusz M. M. Bujnicki posted to cabs casp comparative_modeling strutcture_prediction by mcbla on 2009-04-27 13:16:18 as along with 4 people and 2 groups mijam nigham marcius dgront BioinfoCIPF SGU-CIPF
	Defrosting the frozen approximation: PROSPECTOR - A new approach to threading [My Copy] Proteins: Structure, Function, and Genetics, Vol. 42, No. 3. (2001), pp. 319-331. by Jeffrey Skolnick, Daisuke Kihara posted to comparative_modeling threading by mcbla on 2009-04-26 00:32:48 as along with 1 person j3xucite
	A general method applicable to the search for similarities in the amino acid sequence of two proteins. [My Copy] Journal of molecular biology, Vol. 48, No. 3. (March 1970), pp. 443-453. by S. B. Needleman, C. D. Wunsch posted to comparative_modeling by mcbla on 2009-04-25 23:44:07 as along with 16 people windman83 esyoun stsaft timflutre BioNica db344 DarkMars cawelsh9 sebk jwm dgront rabio incovoma yylin newton1234 Ema
	Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. [My Copy] Nucleic acids research, Vol. 25, No. 17. (1 September 1997), pp. 3389-3402. by S. F. Altschul, T. L. Madden, A. A. Schäffer, et al.J. Zhang, Z. Zhang, W. Miller, D. J. Lipman posted to comparative_modeling by mcbla on 2009-04-25 23:24:11 as along with 68 people and 5 groups rshe niallhaslam ucbcjbm timhubbard parnell tfuji maria_hauser jbhiatt yylin mgomes BioNica idoerg pjcite swp09 kgutwin cpwardell johanviklund daforerog nlapalu sebk tjimenez shung pwais dakelley knaseanka setar iakes miguel kaarsinogen bjorns bicko jmeppley chad_davis balajis nuke2005 eweaver david_parsons indigoviolet dullhunk robert dgront happy_manatee caporaso treangen kengg manzanita CitoJam jdelcampo aengisch rabio massivemayhem mirzazadeh azazello sujaikumar beatrizfernandez GustavoLacerda siebertm adijr viktor21614 mijam grottenolm bandrewfox edvin newton1234 mariakmejia granujilla marti CharlesM References for 3DSim paper EisenLab biomedical-nlp Microbial-Ecology Plantandetc
	Basic local alignment search tool. [My Copy] Journal of molecular biology, Vol. 215, No. 3. (5 October 1990), pp. 403-410. by S. F. Altschul, W. Gish, W. Miller, E. W. Myers, D. J. Lipman posted to comparative_modeling by mcbla on 2009-04-25 23:20:50 as along with 77 people and 6 groups VGreiff richter80 krapnik azazello rshe mtaschuk sjcockell niallhaslam djohnson thegoose humburg timhubbard pachorip n00c maria_hauser rpetrenko parnell yylin esyoun APRegier idoerg Neeperando robert85 thegoose2 daforerog coela alessandroparini bertelsen Blackbeard florisbuijzen laurabailey treangen pwais mmartin tharris dmp camster davidng evaf dragonrez jwm jmeppley Ayest RMGraze ea yas balajis alexg indigoviolet moborg arcticrasta dullhunk dgront caporaso michC myui BioNica CitoJam rabio timflutre lusk cjeans incovoma beatrizfernandez wenhan jtomasch GustavoLacerda sgoetz siebertm ichbins81 jofiel Thaverkamp shung marti ashaytan benwei granujilla C. elegans / WormBase dbk-lab EisenLab T_lab biomedical-nlp Microbial-Ecology
	Practical lessons from protein structure prediction. [My Copy] Nucleic Acids Res, Vol. 33, No. 6. (2005), pp. 1874-1891. by K. Ginalski, N. V. Grishin, A. Godzik, L. Rychlewski posted to comparative_modeling by mcbla on 2009-03-25 13:44:40 as along with 8 people and 4 groups ana aalibes thaliana okarsligil marcius duartemolha dgront mirzazadeh structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
	Global Rigid Body Modeling of Macromolecular Complexes against Small-Angle Scattering Data [My Copy] Biophys. J., Vol. 89, No. 2. (1 August 2005), pp. 1237-1250. by Maxim V. Petoukhov, Dmitri I. Svergun posted to comparative_modeling experimental_restraints saxs by dgront on 2008-12-28 06:24:42 as along with 1 person TOchi
	Comparative modeling for protein structure prediction [My Copy] Current Opinion in Structural Biology, Vol. 16, No. 2. (27 February 2006), pp. 172-177. by Krzysztof Ginalski posted to comparative_modeling by mcbla on 2008-11-24 00:31:32 as along with 8 people mijam BragilMassoud kuhn rabio schuylrp ruvido insectopalo granujilla
	Evaluation of 3D-Jury on CASP7 models [My Copy] BMC Bioinformatics, Vol. 8 (21 August 2007), 304. by László Kaján, Leszek Rychlewski posted to casp comparative_modeling by mcbla on 2008-11-24 00:26:42 as along with 1 person rabio
	Knowledge-based potentials in protein design [My Copy] Current Opinion in Structural Biology In Membranes / Engineering and design, Vol. 16, No. 4. (August 2006), pp. 508-513. by Alan M. Poole, Rama Ranganathan posted to cabs comparative_modeling force_field interaction_hierarchy intro knowledge_based_potentials lattice_model lattice_models modeling mqap prediction protein protein_folding protein_structure review structure strutcture_prediction by mcbla on 2008-11-24 00:25:28 as along with 6 people and 2 groups krapnik flbarroso nigham marcius rabio bethbromley BioinfoCIPF SGU-CIPF
	Protein Folding with a Reduced Model and Inaccurate Short-Range Restraints [My Copy] Macromolecular Theory and Simulations, Vol. 14, No. 7. (2005), pp. 444-451. by Dorota Plewczynska, Andrzej Kolinski posted to comparative_modeling reduced_models restraints by rabio on 2007-12-27 04:12:54 as along with 1 person dgront
	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 comparative_modeling refinement simulation_methods by chenway on 2007-12-06 09:19:02 as along with 16 people and 2 groups bmduggan newton1234 apaydin aheilbut jwm eckart_bindewald ffranca dgront massivemayhem cjeans zwang cactus sobolevnrm boris_aguilar Ema ardalby baker-group OPIG
	Comparative modeling without implicit sequence alignments [My Copy] Bioinformatics, Vol. 23, No. 19. (27 July 2007), pp. 2522-2527. by Andrzej Kolinski, Dominik Gront posted to comparative_modeling sequence_alignment by rabio on 2007-10-25 13:57:57 as along with 2 people carlescorbi sekmi
	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
	Derivation of protein-specific pair potentials based on weak sequence fragment similarity. [My Copy] Proteins, Vol. 38, No. 1. (1 January 2000), pp. 3-16. by J. Skolnick, A. Kolinski, A. Ortiz posted to comparative_modeling force_field by mcbla on 2007-07-08 11:20:54 as along with 2 people and 2 groups marcius dgront BioinfoCIPF SGU-CIPF
	The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models. [My Copy] Nucleic Acids Res, Vol. 32, No. Database issue. (1 January 2004) by J. Kopp, T. Schwede posted to comparative_modeling databases by dgront on 2007-05-07 08:57:31 as along with 1 person flbarroso
	Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection. [My Copy] Nucleic Acids Res, Vol. 34, No. 17. (2006) by D. Chivian, D. Baker posted to comparative_modeling suboptimal_alignment by dgront on 2007-03-01 17:53:10 as along with 2 people jwm rabio
	Relationship between multiple sequence alignments and quality of protein comparative models. [My Copy] Proteins, Vol. 58, No. 1. (1 January 2005), pp. 151-157. by D. Cozzetto, A. Tramontano posted to comparative_modeling sequence_alignment by dgront on 2006-11-04 16:08:26 as along with 1 person ffranca
	Three-dimensional comparative modeling of RNA. [My Copy] Nucleic Acids Symp Ser, No. 36. (1997), pp. 69-71. by C. Zwieb, F. Müller posted to algorithms bioinformatics comparative_modeling rna by marcius to the group SGU-CIPF on 2006-10-27 21:31:25 as along with 1 group BioinfoCIPF
	Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection [My Copy] Nucleic Acids Research, Vol. 34, No. 17. (October 2006), pp. e112-e112. by D. Chivian, D. Baker posted to algorithms bioinformatics comparative_modeling sequence_alignment by marcius to the group SGU-CIPF on 2006-10-25 21:43:08 as along with 1 person and 1 group j3xucite BioinfoCIPF
	Structural Modeling of Protein Interactions by Analogy: Application to PSD-95 [My Copy] PLoS Computational Biology, Vol. preprint, No. 2006. (1 October 2006) by Dmitry Korkin, Fred P. Davis, Frank Alber, et al.Tinh Luong, Min-Yi Shen, Vladan Lucic, Mary B. Kennedy, Andrej Sali posted to algorithms comparative_docking comparative_modeling protein_domains protein_interactions by marcius on 2006-10-22 12:12:40 as along with 2 groups BioinfoCIPF SGU-CIPF
	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
	Protein structure modeling for structural genomics. [My Copy] Nat Struct Biol, Vol. 7 Suppl (November 2000), pp. 986-990. by R. Sánchez, U. Pieper, F. Melo, et al.N. Eswar, M. A. Martí-Renom, M. S. Madhusudhan, N. Mirković, A. Sali posted to comparative_modeling structural_genomics by dgront on 2006-08-28 17:18:41 as along with 2 people and 2 groups marcius penka BioinfoCIPF SGU-CIPF
	Target practice. [My Copy] Nat Struct Biol, Vol. 8, No. 6. (June 2001), pp. 482-484. by A. Sali posted to comparative_modeling structural_genomics by dgront on 2006-08-28 16:24:48 as
	From words to literature in structural proteomics. [My Copy] Nature, Vol. 422, No. 6928. (13 March 2003), pp. 216-225. by A. Sali, R. Glaeser, T. Earnest, W. Baumeister posted to comparative_modeling proteomics review structural_genomics by dgront on 2006-08-16 17:35:53 as along with 6 people tomhebbron bicko chad_davis ruvido lpfernandes higueruelo
	MODBASE, a database of annotated comparative protein structure models, and associated resources. [My Copy] Nucleic acids research, Vol. 32, No. Database issue. (1 January 2004) by Ursula Pieper, Narayanan Eswar, Hannes Braberg, et al.M. S. Madhusudhan, Fred P. Davis, Ashley C. Stuart, Nebojsa Mirkovic, Andrea Rossi, Marc A. Marti-Renom, Andras Fiser, Ben Webb, Daniel Greenblatt, Conrad C. Huang, Thomas E. Ferrin, Andrej Sali posted to comparative_modeling databases by dgront on 2006-08-02 13:42:31 as along with 4 people and 2 groups tjimenez pjcite marcius blackbart BioinfoCIPF SGU-CIPF
	High-throughput computational and experimental techniques in structural genomics. [My Copy] Genome Res, Vol. 14, No. 10B. (October 2004), pp. 2145-2154. by M. R. Chance, A. Fiser, A. Sali, et al.U. Pieper, N. Eswar, G. Xu, J. E. Fajardo, T. Radhakannan, N. Marinkovic posted to comparative_modeling experimental review structural_genomics by dgront on 2006-07-31 18:55:09 as along with 2 people flbarroso vavi
	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 comparative_modeling protein strutcture_prediction by vavi on 2006-07-31 13:48:24 as along with 12 people and 2 groups chemrahul82 paddydu Diego_Prada reyez guxiyou ana jwm wouterboomsma j3xucite hmk mijam joule structural_bioinformatics Bioinformatics
	Tools for comparative protein structure modeling and analysis. [My Copy] Nucleic Acids Res, Vol. 31, No. 13. (1 July 2003), pp. 3375-3380. by N. Eswar, B. John, N. Mirkovic, et al.A. Fiser, V. A. Ilyin, U. Pieper, A. C. Stuart, M. A. Marti-Renom, M. S. Madhusudhan, B. Yerkovich, A. Sali posted to comparative_modeling protein strutcture_prediction by vavi on 2006-07-25 14:23:56 as along with 2 people and 2 groups chad_davis marcius BioinfoCIPF SGU-CIPF
	Reliability of assessment of protein structure prediction methods. [My Copy] Structure (Camb), Vol. 10, No. 3. (March 2002), pp. 435-440. by M. A. Marti-Renom, M. S. Madhusudhan, A. Fiser, B. Rost, A. Sali posted to casp comparative_modeling by dgront on 2006-07-17 16:58:59 as along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
	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 comparative_modeling fragments by dgront on 2006-06-29 14:37:03 as along with 2 people and 1 group mijam Einat structural_bioinformatics
	The Relationship Between Sequence and Interaction Divergence in Proteins [My Copy] Journal of Molecular Biology, Vol. 332, No. 5. (3 October 2003), pp. 989-998. by Patrick Aloy, Hugo Ceulemans, Alexander Stark, Robert B. Russell posted to comparative_modeling protein_interaction protein_structure by ana on 2006-06-27 22:25:06 as along with 4 people and 2 groups pansapiens eweaver Evangelia RebeccaHamer structural_bioinformatics Bioinformatics
	MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading. [My Copy] Proteins, Vol. 49, No. 3. (15 November 2002), pp. 350-364. by L. Lu, H. Lu, J. Skolnick posted to comparative_modeling protein_interaction protein_structure by ana to the group Bioinformatics on 2006-06-27 21:38:38 as along with 6 people and 4 groups bicko chad_davis marcius sangeetha ruvido kgutwin structural_bioinformatics insilicodrug BioinfoCIPF SGU-CIPF
	Interrogating protein interaction networks through structural biology [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 9. (30 April 2002), pp. 5896-5901. by Patrick Aloy, Robert B. Russell posted to comparative_modeling protein_interaction protein_structure by ana to the group structural_bioinformatics on 2006-06-27 21:36:03 as along with 15 people and 2 groups beete aceol kgutwin tomhebbron bpcusack barry baaden bicko lfriedl chad_davis henschel ruvido cjeans tale Evangelia kdl Bioinformatics
	Using known substructures in protein model building and crystallography. [My Copy] EMBO J, Vol. 5, No. 4. (April 1986), pp. 819-822. by T. A. Jones, S. Thirup posted to atom_reconstruction comparative_modeling by dgront on 2006-06-21 13:25:32 as along with 2 people and 2 groups krapnik jwm Radiation_Damage Stressosome
	18th Sir Hans Krebs lecture. Knowledge-based protein modelling and design. [My Copy] European journal of biochemistry / FEBS, Vol. 172, No. 3. (15 March 1988), pp. 513-520. by T. Blundell, D. Carney, S. Gardner, et al.F. Hayes, B. Howlin, T. Hubbard, J. Overington, D. A. Singh, B. L. Sibanda, M. Sutcliffe posted to atom_reconstruction comparative_modeling by dgront on 2006-06-21 13:21:40 as along with 1 person timhubbard
	Physically realistic homology models built with ROSETTA can be more accurate than their templates. [My Copy] Proc Natl Acad Sci U S A, Vol. 103, No. 14. (4 April 2006), pp. 5361-5366. by K. M. Misura, D. Chivian, C. A. Rohl, D. E. Kim, D. Baker posted to comparative_modeling rosetta by dgront on 2006-06-20 16:18:56 as along with 7 people krapnik kgutwin j3xucite jwm balajis bilab BioNica
	Protein structure prediction constrained by solution X-ray scattering data and structural homology identification. [My Copy] J Mol Biol, Vol. 316, No. 1. (8 February 2002), pp. 173-187. by W. Zheng, S. Doniach posted to comparative_modeling experimental by dgront on 2006-06-13 12:36:00 as along with 1 person thamelry
	Combining electron microscopy and comparative protein structure modeling. [My Copy] Curr Opin Struct Biol, Vol. 15, No. 5. (October 2005), pp. 578-585. by M. Topf, A. Sali posted to comparative_modeling experimental review by dgront on 2006-06-12 18:51:28 as
	Completeness in structural genomics. [My Copy] Nat Struct Biol, Vol. 8, No. 6. (June 2001), pp. 559-566. by D. Vitkup, E. Melamud, J. Moult, C. Sander posted to comparative_modeling by dgront on 2006-06-12 18:07:08 as
	Prediction of local structure in proteins using a library of sequence-structure motifs. [My Copy] Journal of molecular biology, Vol. 281, No. 3. (21 August 1998), pp. 565-577. by C. Bystroff, D. Baker posted to comparative_modeling by dgront on 2006-05-25 14:14:04 as along with 2 people jwm wouterboomsma
	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 comparative_modeling rosetta by dgront on 2006-05-25 14:13:01 as along with 7 people mijam granujilla bullli502 nigham thaliana JimmyMac saunders
	Fragment Ranking in Modelling of Protein Structure : Conformationally Constrained Environmental Amino Acid Substitution Tables [My Copy] Journal of Molecular Biology, Vol. 229, No. 1. (5 January 1993), pp. 194-220. by Christopher M. Topham, Alasdair Mcleod, Frank Eisenmenger, John P. Overington, Mark S. Johnson, Tom L. Blundell posted to comparative_modeling databases by dgront on 2006-05-24 17:48:38 as along with 5 people viktor21614 bicko vavi medic0747 sebk
	ProMod and Swiss-Model: Internet-based tools for automated comparative protein modelling. [My Copy] Biochem Soc Trans, Vol. 24, No. 1. (February 1996), pp. 274-279. by M. C. Peitsch posted to comparative_modeling server by dgront on 2006-05-24 17:02:43 as
	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 comparative_modeling server by dgront on 2006-05-24 17:01:04 as along with 9 people krapnik flbarroso shacko sebk bpb ffranca gelack Haggan granujilla

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protein_structure	43
structure_prediction	40
casp	21
cafasp	18
bioinformatics	15
biophysics	15
model_assessment	12
review	12
algorithms	9
evolution	9
protein_interaction	9
structure	7
ab-initio	6
protein_sequence	6
rna	6
sequence_alignment	5
force_field	4
protein_folding	4
structural_genomics	4
strutcture_prediction	4
clustering	3
comparative_docking	3
computational_biology	3
databases	3
experimental	3
model_refinement	3
molecular_mimicry	3
multiple_structure_comparison	3
pca	3
protein	3
protein_design	3
protein_domains	3
protein_evolution	3
protein_fragments	3
protein_interactions	3
rosetta	3
secondary_structure	3
structure_comparison	3
structure_fragments	3
atom_reconstruction	2
cabs	2
mqap	2
refinement	2
restraints	2
server	2
simulation_methods	2
threading	2
tools	2
experimental_restraints	1
fold_recognition	1
fragments	1
hmm	1
interaction_hierarchy	1
intro	1
knowledge_based_potentials	1
lattice_model	1
lattice_models	1
modeling	1
pfc3	1
prediction	1
proteomics	1
reduced_models	1
rotamers	1
saxs	1
statistical_potentials	1
structure_similarity	1
suboptimal_alignment	1
svm	1

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