Group: BioinfoCIPF - with tag structure_prediction [64 articles] Export

Recent papers posted by members of the BioinfoCIPF group with tag structure_prediction

	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 structure_prediction rna ab-initio by marcius to the group BioinfoCIPF on 2007-09-01 10:46:02 as along with 8 people and 1 group fisherp rsaito jwm eckart_bindewald zwang physics Ema reyez 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 BioinfoCIPF on 2006-09-07 13:31:07 as along with 1 person and 1 group eckart_bindewald SGU-CIPF
	Prediction of protein three-dimensional structures in insertion and deletion regions: a procedure for searching data bases of representative protein fragments using geometric scoring criteria. [My Copy] J Mol Biol, Vol. 253, No. 1. (13 October 1995), pp. 114-131. by T. Fechteler, U. Dengler, D. Schomburg posted to bioinformatics protein_fragments structure_prediction by marcius to the group BioinfoCIPF on 2006-05-19 18:30:30 as along with 2 people and 3 groups ana GermanErlenkamp structural_bioinformatics Bioinformatics SGU-CIPF
	Facilitating RNA structure prediction with microarrays. [My Copy] Biochemistry, Vol. 45, No. 2. (17 January 2006), pp. 581-593. by E. Kierzek, R. Kierzek, D. H. Turner, I. E. Catrina posted to microarray rna secondary_structure structure_prediction by marcius to the group BioinfoCIPF on 2006-05-18 00:58:23 as along with 1 person and 2 groups condon beta SGU-CIPF
	Derivation of rules for comparative protein modeling from a database of protein structure alignments. [My Copy] Protein Sci, Vol. 3, No. 9. (September 1994), pp. 1582-1596. by A. Sali, J. P. Overington posted to bioinformatics biophysics comparative_modeling structure_prediction by marcius to the group BioinfoCIPF on 2006-04-08 07:26:12 as along with 2 people and 3 groups ana bicko structural_bioinformatics Bioinformatics SGU-CIPF
	Towards genome-scale structure prediction for transmembrane proteins. [My Copy] Philos Trans R Soc Lond B Biol Sci, Vol. 361, No. 1467. (29 March 2006), pp. 465-475. by N. Hurwitz, M. Pellegrini-Calace, D. T. Jones posted to computational_biology membrane_protein structure_prediction by marcius to the group BioinfoCIPF on 2006-03-15 22:59:20 as along with 1 person and 1 group thaliana SGU-CIPF
	Modeling the three-dimensional structure of RNA. [My Copy] FASEB J, Vol. 7, No. 1. (January 1993), pp. 97-105. by D. Gautheret, R. Cedergren posted to computational_biology rna structure_prediction by marcius to the group BioinfoCIPF on 2006-02-11 01:12:07 as along with 1 person and 1 group eckart_bindewald SGU-CIPF
	High-resolution protein folding with a transferable potential [My Copy] PNAS, Vol. 102, No. 52. (27 December 2005), pp. 18914-18919. by Isaac A. Hubner, Eric J. Deeds, Eugene I. Shakhnovich posted to ab-initio biophysics protein_structure structure_prediction by marcius to the group BioinfoCIPF on 2006-02-07 02:17:31 as along with 1 group SGU-CIPF
	The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. [My Copy] Bioinformatics (Oxford, England), Vol. 22, No. 2. (15 January 2006), pp. 195-201. by K. Arnold, L. Bordoli, J. Kopp, T. Schwede posted to algorithms protein_structure servers structure_prediction by marcius to the group BioinfoCIPF on 2006-02-02 05:48:58 as along with 5 people and 1 group krapnik flbarroso hervelequere chad_davis ffranca SGU-CIPF
	Grow to Fit Molecular Dynamics (G2FMD): an ab initio method for protein side-chain assignment and refinement [My Copy] Protein Engineering, Design and Selection, Vol. 19, No. 2. (February 2006), pp. 55-65. by Wei Zhang, Yong Duan posted to ab-initio algorithms biophysics computational_biology protein_structure structure_prediction by marcius to the group BioinfoCIPF on 2006-01-27 01:13:40 as along with 1 group SGU-CIPF
	Combining evolutionary and structural information for local protein structure prediction. [My Copy] Proteins, Vol. 56, No. 4. (1 September 2004), pp. 782-794. by J. Pei, N. V. Grishin posted to bioinformatics biophysics sequence_alignment statistical_potentials structure_prediction by marcius to the group BioinfoCIPF on 2006-01-20 23:19:35 as along with 1 group SGU-CIPF
	Five hierarchical levels of sequence-structure correlation in proteins. [My Copy] Applied bioinformatics. , Vol. 3, No. 2-3. (2004), pp. 97-104. by C. Bystroff, Y. Shao, X. Yuan posted to bioinformatics biophysics sequence-structure sequence_alignment statistical_potentials structure_prediction by marcius to the group BioinfoCIPF on 2006-01-20 23:13:49 as along with 3 people and 1 group flbarroso eweaver rabio SGU-CIPF
	Evolutionarily Conserved Pathways of Energetic Connectivity in Protein Families [My Copy] Science, Vol. 286, No. 5438. (8 October 1999), pp. 295-299. by Steve W. Lockless, Rama Ranganathan posted to bioinformatics biophysics sequence_alignment statistical_potentials structure_prediction by marcius to the group BioinfoCIPF on 2006-01-20 23:11:47 as along with 18 people and 5 groups krapnik mgomes qluo stevanspringer Einat eckart_bindewald analogAI dgront caporaso sriram_s choonpeng Haggan rabio mottonen zambujo mingzhi bethbromley ca3295 Marcotte_Lab structural_bioinformatics FAB-lab biomedical-nlp SGU-CIPF
	Evolutionarily conserved networks of residues mediate allosteric communication in proteins [My Copy] Nature Structural & Molecular Biology, Vol. 10, No. 1. (16 December 2002), pp. 59-69. by Gurol M. Suel, Steve W. Lockless, Mark A. Wall, Rama Ranganathan posted to bioinformatics biophysics sequence_alignment statistical_potentials structure_prediction by marcius to the group BioinfoCIPF on 2006-01-20 23:09:56 as along with 20 people and 2 groups mgomes qluo arjun_citeulike RebeccaHamer ynaito lna dimka eckart_bindewald gbart analogAI nirfriedman dgront caporaso choonpeng efge carlescorbi mingzhi yalexeev weisblum ca3295 biomedical-nlp SGU-CIPF
	Local complexity of amino acid interactions in a protein core. [My Copy] Proc Natl Acad Sci U S A, Vol. 101, No. 1. (6 January 2004), pp. 111-116. by R. K. Jain, R. Ranganathan posted to bioinformatics biophysics sequence_alignment statistical_potentials structure_prediction by marcius to the group BioinfoCIPF on 2006-01-20 23:08:01 as along with 5 people and 3 groups ana barry lna gbart choonpeng structural_bioinformatics Bioinformatics SGU-CIPF
	Natural-like function in artificial WW domains [My Copy] Nature, Vol. 437, No. 7058., pp. 579-583. by William P. Russ, Drew M. Lowery, Prashant Mishra, Michael B. Yaffe, Rama Ranganathan posted to bioinformatics biophysics sequence_alignment statistical_potentials structure_prediction by marcius to the group BioinfoCIPF on 2006-01-20 23:06:18 as along with 6 people and 4 groups ana barry balajis caporaso bethbromley ca3295 structural_bioinformatics Bioinformatics biomedical-nlp SGU-CIPF
	The SWISS-MODEL Repository: new features and functionalities. [My Copy] Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006) by J. Kopp, T. Schwede posted to databases protein_structure structure_prediction by marcius to the group BioinfoCIPF on 2006-01-13 23:58:03 as along with 1 person and 1 group miguel SGU-CIPF
	Modeling RNA tertiary structure from patterns of sequence variation. [My Copy] Methods Enzymol, Vol. 317 (2000), pp. 491-510. by F. Michel, M. Costa, C. Massire, E. Westhof posted to review rna structure_prediction by marcius to the group BioinfoCIPF on 2005-12-22 22:45:59 as along with 1 group SGU-CIPF
	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 cafasp casp comparative_modeling model_assessment structure_prediction by marcius to the group BioinfoCIPF on 2005-12-22 06:53:06 as along with 8 people and 3 groups mcbla ana aalibes thaliana okarsligil duartemolha dgront mirzazadeh structural_bioinformatics Bioinformatics SGU-CIPF
	Protein structure prediction in genomics. [My Copy] Brief Bioinform, Vol. 2, No. 2. (May 2001), pp. 111-125. by D. T. Jones posted to review structural_genomics structure_prediction by marcius to the group BioinfoCIPF on 2005-12-22 06:51:11 as along with 1 group SGU-CIPF
	Structural genomics analysis of alternative splicing and application to isoform structure modeling. [My Copy] Proc Natl Acad Sci U S A (14 December 2005) by Peng Wang, Bo Yan, Jun-Tao T. Guo, Chindo Hicks, Ying Xu posted to bioinformatics evolution sequence structural_genomics structure_prediction by marcius to the group BioinfoCIPF on 2005-12-22 03:26:15 as along with 4 people and 1 group Cortel shuns penka antonkratz SGU-CIPF
	Protein Structure Prediction: Inroads to Biology [My Copy] Molecular Cell, Vol. 20, No. 6. (22 December 2005), pp. 811-819. by Donald Petrey, Barry Honig posted to bioinformatics folding protein_structure review structure_prediction by marcius to the group BioinfoCIPF on 2005-12-22 00:53:03 as along with 4 people and 1 group pansapiens vavi penka Haggan SGU-CIPF
	The relation between the divergence of sequence and structure in proteins. [My Copy] The EMBO journal, Vol. 5, No. 4. (April 1986), pp. 823-826. by C. Chothia, A. M. Lesk posted to evolution structure structure_alignment structure_prediction by marcius to the group BioinfoCIPF on 2005-12-20 00:56:52 as along with 16 people and 5 groups edvin parnell dfdong martainn ucbcjbm bertelsen semin sgoetz cen4ik ana pansapiens jwm Einat xdeupi ffranca insectopalo structural_bioinformatics Radiation_Damage Stressosome Bioinformatics SGU-CIPF
	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 ab-initio biophysics computational_biology structure_prediction by marcius to the group BioinfoCIPF on 2005-11-02 09:16:25 as along with 11 people and 3 groups ucbcjbm paddydu kgutwin BragilMassoud ana barry thaliana jwm vavi gbart thamelry structural_bioinformatics Bioinformatics SGU-CIPF
	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 ab-initio bioinformatics biophysics cafasp comparative_modeling review structure_prediction by marcius to the group BioinfoCIPF on 2005-10-28 00:14:41 as along with 18 people and 2 groups krapnik rabio ucbcjbm paddydu flbarroso thaliana jwm vavi bicko KyuhoLee eweaver tny nickolay dgront rsantana mirzazadeh insectopalo barry SGU-CIPF structural_bioinformatics
	Structure-derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds. [My Copy] J Mol Biol, Vol. 224, No. 3. (5 April 1992), pp. 725-732. by G. Casari, M. J. Sippl posted to computational_biology review statistical_potentials structure_prediction by marcius to the group BioinfoCIPF on 2005-10-26 19:19:29 as along with 1 group SGU-CIPF
	Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures. [My Copy] J Comput Aided Mol Des, Vol. 7, No. 4. (August 1993), pp. 473-501. by M. J. Sippl posted to computational_biology review statistical_potentials structure_prediction by marcius to the group BioinfoCIPF on 2005-10-26 19:19:19 as along with 3 people and 1 group dgront aengisch mcbla SGU-CIPF
	Knowledge-based potentials for proteins. [My Copy] Curr Opin Struct Biol, Vol. 5, No. 2. (April 1995), pp. 229-235. by M. J. Sippl posted to computational_biology review statistical_potentials structure_prediction by marcius to the group BioinfoCIPF on 2005-10-26 19:19:08 as along with 4 people and 1 group chad_davis eckart_bindewald tolot27 janasont SGU-CIPF
	Threading thrills and threats. [My Copy] Structure, Vol. 4, No. 1. (15 January 1996), pp. 15-19. by M. J. Sippl, H. Flöckner posted to computational_biology review statistical_potentials structure_prediction by marcius to the group BioinfoCIPF on 2005-10-26 19:18:59 as along with 1 group SGU-CIPF
	Empirical potentials and functions for protein folding and binding. [My Copy] Curr Opin Struct Biol, Vol. 7, No. 2. (April 1997), pp. 222-228. by S. Vajda, M. Sippl, J. Novotny posted to computational_biology review statistical_potentials structure_prediction by marcius to the group BioinfoCIPF on 2005-10-26 19:18:50 as along with 2 people and 1 group kgutwin chad_davis SGU-CIPF
	Theory and simulation. Old problems, new paradigms. [My Copy] Curr Opin Struct Biol, Vol. 7, No. 2. (April 1997), pp. 179-180. by J. Novotny, M. Sippl posted to computational_biology review statistical_potentials structure_prediction by marcius to the group BioinfoCIPF on 2005-10-26 19:18:40 as along with 1 group SGU-CIPF
	The role of protein structure in genomics. [My Copy] FEBS Lett, Vol. 476, No. 1-2. (30 June 2000), pp. 98-102. by F. S. Domingues, W. A. Koppensteiner, M. J. Sippl posted to computational_biology review statistical_potentials structural_genomics structure_prediction by marcius to the group BioinfoCIPF on 2005-10-26 19:18:29 as along with 1 group SGU-CIPF
	Knowledge-based potentials--back to the roots. [My Copy] Biochemistry (Mosc), Vol. 63, No. 3. (March 1998), pp. 247-252. by W. A. Koppensteiner, M. J. Sippl posted to computational_biology review statistical_potentials structure_prediction by marcius to the group BioinfoCIPF on 2005-10-26 19:18:16 as along with 1 person and 1 group tolot27 SGU-CIPF
	Assessment of CASP6 predictions for new and nearly new fold targets. [My Copy] Proteins (26 September 2005) by James J J. Vincent, Chin-Hsien H. Tai, B K K. Sathyanarayana, Byungkook Lee posted to ab-initio cafasp casp model_evaluation structure_prediction by marcius to the group BioinfoCIPF on 2005-10-22 09:12:32 as along with 1 person and 1 group nigham SGU-CIPF
	Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models. [My Copy] Proteins (26 September 2005) by Andrzej Koliński, Janusz M M. Bujnicki posted to ab-initio bioinformatics comparative_modeling model_assessment structure_prediction by marcius to the group BioinfoCIPF on 2005-10-22 09:12:12 as along with 5 people and 1 group rabio mijam mcbla nigham dgront SGU-CIPF
	Protein structure prediction in CASP6 using CHIMERA and FAMS. [My Copy] Proteins (26 September 2005) by Mayuko Takeda-Shitaka, Genki Terashi, Daisuke Takaya, Kazuhiko Kanou, Mitsuo Iwadate, Hideaki Umeyama posted to bioinformatics cafasp casp sequence_alignment structure_prediction by marcius to the group BioinfoCIPF on 2005-10-22 09:11:43 as along with 1 group SGU-CIPF
	Protein structure prediction using a variety of profile libraries and 3D verification. [My Copy] Proteins (26 September 2005) by Kentaro Tomii, Takatsugu Hirokawa, Chie Motono posted to bioinformatics cafasp casp model_assessment structure_prediction by marcius to the group BioinfoCIPF on 2005-10-22 09:11:09 as along with 1 group SGU-CIPF
	SAM-T04: what's new in protein-structure prediction for CASP6. [My Copy] Proteins (26 September 2005) by Kevin Karplus, Sol Katzman, George Shackleford, et al.Martina Koeva, Jenny Draper, Bret Barnes, Marcia Soriano, Richard Hughey posted to cafasp casp sequence_alignment structure_prediction by marcius to the group BioinfoCIPF on 2005-10-22 09:10:38 as along with 1 group SGU-CIPF
	Protein loop structure prediction with flexible stem geometries. [My Copy] Proteins (12 October 2005) by M Mönnigmann, C A A. Floudas posted to cafasp casp loop_modeling protein_structure structure_prediction by marcius to the group BioinfoCIPF on 2005-10-22 09:06:47 as along with 1 person and 1 group vavi SGU-CIPF
	Assessment of predictions submitted for the CASP6 comparative modelling category. [My Copy] Proteins (26 September 2005) by Michael Tress, Iakes Ezkurdia, Osvaldo Graña, Gonzalo López, Alfonso Valencia posted to cafasp casp comparative_modeling protein_structure structure_prediction by marcius to the group BioinfoCIPF on 2005-10-22 08:59:31 as along with 3 people and 1 group nigham ffranca magia215 SGU-CIPF
	Free modeling with Rosetta in CASP6. [My Copy] Proteins (26 September 2005) by Philip Bradley, Lars Malmström, Bin Qian, et al.Jack Schonbrun, Dylan Chivian, David E E. Kim, Jens Meiler, Kira M S M. Misura, David Baker posted to ab-initio cafasp casp structure_prediction by marcius to the group BioinfoCIPF on 2005-10-22 08:58:20 as along with 6 people and 1 group krapnik saunders jwm dgront schuylrp mirzazadeh SGU-CIPF
	Prediction of novel and analogous folds using fragment assembly and fold recognition. [My Copy] Proteins (26 September 2005) by D T T. Jones, K Bryson, A Coleman, et al.L J J. McGuffin, M I I. Sadowski, J S S. Sodhi, J J J. Ward posted to cafasp casp comparative_modeling model_assessment protein_fragments protein_structure structure_prediction by marcius to the group BioinfoCIPF on 2005-10-22 08:57:29 as along with 1 group SGU-CIPF
	SPARKS 2 and SP(3) servers in CASP 6. [My Copy] Proteins (26 September 2005) by Hongyi Zhou, Yaoqi Zhou posted to cafasp casp comparative_modeling model_assessment protein_structure structure_prediction by marcius to the group BioinfoCIPF on 2005-10-22 08:56:27 as along with 1 person and 1 group j3xucite SGU-CIPF
	Progress over the first decade of CASP experiments. [My Copy] Proteins (26 September 2005) by Andriy Kryshtafovych, Ceslovas Venclovas, Krzysztof Fidelis, John Moult posted to casp review structure_prediction by marcius to the group BioinfoCIPF on 2005-10-22 08:55:22 as along with 5 people and 1 group saunders bicko ffranca schuylrp granujilla SGU-CIPF
	Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation. [My Copy] Proc Natl Acad Sci U S A, Vol. 101, No. 43. (26 October 2004), pp. 15346-15351. by B. Qian, A. R. Ortiz, D. Baker posted to biophysics clustering comparative_modeling protein_structure structure_prediction by marcius to the group BioinfoCIPF on 2005-10-22 05:00:32 as along with 6 people and 3 groups krapnik aqeel ana barry lna dgront structural_bioinformatics Bioinformatics SGU-CIPF
	Have we seen all structures corresponding to short protein fragments in the Protein Data Bank? An update. [My Copy] Protein Eng, Vol. 16, No. 6. (June 2003), pp. 407-414. by P. Du, M. Andrec, R. M. Levy posted to protein_fragments structure_prediction by marcius to the group BioinfoCIPF on 2005-10-22 03:09:41 as along with 1 group SGU-CIPF
	Structure prediction of membrane proteins. [My Copy] Genomics Proteomics Bioinformatics, Vol. 2, No. 1. (February 2004), pp. 1-5. by C. Zhou, Y. Zheng, Y. Zhou posted to membrane_protein protein_structure structure_prediction by marcius to the group BioinfoCIPF on 2005-10-22 03:09:41 as along with 1 group SGU-CIPF
	State-of-the-art in membrane protein prediction. [My Copy] Appl Bioinformatics, Vol. 1, No. 1. (2002), pp. 21-35. by C. P. Chen, B. Rost posted to membrane_protein protein_structure review structure_prediction by marcius to the group BioinfoCIPF on 2005-10-22 03:09:41 as along with 1 group SGU-CIPF
	Hamiltonians for protein tertiary structure prediction based on three-dimensional environment principles. [My Copy] J Mol Biol, Vol. 233, No. 3. (October 1993), pp. 480-487. by T. Madej, M. C. Mossing posted to algorithms computational_biology protein_structure structure_prediction by marcius to the group BioinfoCIPF on 2005-10-22 03:09:41 as along with 1 group SGU-CIPF
	Computational analysis of alpha-helical membrane protein structure: implications for the prediction of 3D structural models. [My Copy] Protein Eng Des Sel, Vol. 17, No. 8. (August 2004), pp. 613-624. by T. A. Eyre, L. Partridge, J. M. Thornton posted to computational_biology membrane_protein protein_structure structure_prediction by marcius to the group BioinfoCIPF on 2005-10-22 03:09:41 as along with 1 group SGU-CIPF

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protein_structure	101
review	49
bioinformatics	47
statistical_potentials	43
comparative_modeling	41
casp	40
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
cabs	3
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
chemical_shift	2
de_novo	2
dec09	2
enhanced_sampling	2
fold_recognition	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
blast_search	1
disulfide	1
knowledge-based_potentials	1
protein_homology	1
psi_blast	1
similarity	1
unread	1
wide_choice	1

Group: BioinfoCIPF - with tag structure_prediction [64 articles] Export

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