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Group: SGU-CIPF - with tag structure_prediction [64 articles]

Recent papers posted by members of the SGU-CIPF group with tag structure_prediction
  • Automated de novo prediction of native-like RNA tertiary structures
    PNAS (28 August 2007), 0703836104.
    by Rhiju Das, David Baker
    posted to structure_prediction rna ab-initio by marcius to the group SGU-CIPF on 2007-09-01 10:46:02 as ** along with 6 people and 1 group reyez jwm eckart_bindewald zwang physics Ema BioinfoCIPF
  • Computer modeling 16 S ribosomal RNA
    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
  • 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.
    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 SGU-CIPF on 2006-05-19 18:30:30 as ** along with 2 people and 3 groups GermanErlenkamp ana structural_bioinformatics Bioinformatics BioinfoCIPF
  • Facilitating RNA structure prediction with microarrays.
    Biochemistry, Vol. 45, No. 2. (17 January 2006), pp. 581-593.
    by E Kierzek, R Kierzek, DH Turner, IE Catrina
    posted to microarray rna secondary_structure structure_prediction by marcius to the group SGU-CIPF on 2006-05-18 00:58:23 as ** along with 1 person and 2 groups condon beta BioinfoCIPF
  • Derivation of rules for comparative protein modeling from a database of protein structure alignments.
    Protein Sci, Vol. 3, No. 9. (September 1994), pp. 1582-1596.
    by A Sali, JP Overington
    posted to bioinformatics biophysics comparative_modeling structure_prediction by marcius to the group SGU-CIPF on 2006-04-08 07:26:12 as ** along with 2 people and 3 groups ana bicko structural_bioinformatics Bioinformatics BioinfoCIPF
  • Towards genome-scale structure prediction for transmembrane proteins.
    Philos Trans R Soc Lond B Biol Sci, Vol. 361, No. 1467. (29 March 2006), pp. 465-475.
    by N Hurwitz, M Pellegrini-Calace, DT Jones
    posted to computational_biology membrane_protein structure_prediction by marcius to the group SGU-CIPF on 2006-03-15 22:59:20 as ** along with 1 person and 1 group thaliana BioinfoCIPF
  • Modeling the three-dimensional structure of RNA.
    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 SGU-CIPF on 2006-02-11 01:12:07 as ** along with 1 person and 1 group eckart_bindewald BioinfoCIPF
  • High-resolution protein folding with a transferable potential
    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 SGU-CIPF on 2006-02-07 02:17:31 as ** along with 1 group BioinfoCIPF
  • The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling
    Bioinformatics, Vol. 22, No. 2. (15 January 2006), pp. 195-201.
    by Konstantin Arnold, Lorenza Bordoli, Jurgen Kopp, Torsten Schwede
    posted to algorithms protein_structure servers structure_prediction by marcius to the group SGU-CIPF on 2006-02-02 05:48:58 as ** along with 2 people and 1 group chad_davis ffranca BioinfoCIPF
  • Grow to Fit Molecular Dynamics (G2FMD): an ab initio method for protein side-chain assignment and refinement
    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 SGU-CIPF on 2006-01-27 01:13:40 as ** along with 1 group BioinfoCIPF
  • Combining evolutionary and structural information for local protein structure prediction.
    Proteins, Vol. 56, No. 4. (1 September 2004), pp. 782-794.
    by J Pei, NV Grishin
    posted to bioinformatics biophysics sequence_alignment statistical_potentials structure_prediction by marcius to the group SGU-CIPF on 2006-01-20 23:19:35 as ** along with 1 group BioinfoCIPF
  • Five hierarchical levels of sequence-structure correlation in proteins.
    Appl 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 SGU-CIPF on 2006-01-20 23:13:49 as ** along with 2 people and 1 group eweaver rabio BioinfoCIPF
  • Evolutionarily Conserved Pathways of Energetic Connectivity in Protein Families
    Science, Vol. 286, No. 5438. (08 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 SGU-CIPF on 2006-01-20 23:11:47 as ** along with 15 people and 4 groups stevanspringer Einat eckart_bindewald analogAI dgront caporaso sriram_s choonpeng Haggan rabio mottonen zambujo mingzhi bethbromley ca3295 structural_bioinformatics FAB-lab biomedical-nlp BioinfoCIPF
  • Evolutionarily conserved networks of residues mediate allosteric communication in proteins.
    Nat Struct Biol, Vol. 10, No. 1. (January 2003), pp. 59-69.
    by GM Süel, SW Lockless, MA Wall, R Ranganathan
    posted to bioinformatics biophysics sequence_alignment statistical_potentials structure_prediction by marcius to the group SGU-CIPF on 2006-01-20 23:09:56 as ** along with 15 people and 2 groups ca3295 lna dimka eckart_bindewald gbart analogAI nirfriedman dgront caporaso choonpeng efge carlescorbi mingzhi yalexeev weisblum biomedical-nlp BioinfoCIPF
  • Local complexity of amino acid interactions in a protein core.
    Proc Natl Acad Sci U S A, Vol. 101, No. 1. (6 January 2004), pp. 111-116.
    by RK Jain, R Ranganathan
    posted to bioinformatics biophysics sequence_alignment statistical_potentials structure_prediction by marcius to the group SGU-CIPF on 2006-01-20 23:08:01 as ** along with 5 people and 3 groups ana barry lna gbart choonpeng structural_bioinformatics Bioinformatics BioinfoCIPF
  • Natural-like function in artificial WW domains
    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 SGU-CIPF 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 BioinfoCIPF
  • The SWISS-MODEL Repository: new features and functionalities.
    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 SGU-CIPF on 2006-01-13 23:58:03 as ** along with 1 person and 1 group miguel BioinfoCIPF
  • Modeling RNA tertiary structure from patterns of sequence variation.
    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 SGU-CIPF on 2005-12-22 22:45:59 as ** along with 1 group BioinfoCIPF
  • Practical lessons from protein structure prediction.
    Nucleic Acids Res, Vol. 33, No. 6. (2005), pp. 1874-1891.
    by K Ginalski, NV Grishin, A Godzik, L Rychlewski
    posted to cafasp casp comparative_modeling model_assessment structure_prediction by marcius to the group SGU-CIPF on 2005-12-22 06:53:06 as ** along with 7 people and 3 groups ana aalibes thaliana okarsligil duartemolha dgront mirzazadeh structural_bioinformatics Bioinformatics BioinfoCIPF
  • Protein structure prediction in genomics.
    Brief Bioinform, Vol. 2, No. 2. (May 2001), pp. 111-125.
    by DT Jones
    posted to review structural_genomics structure_prediction by marcius to the group SGU-CIPF on 2005-12-22 06:51:11 as ** along with 1 group BioinfoCIPF
  • Structural genomics analysis of alternative splicing and application to isoform structure modeling.
    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 SGU-CIPF on 2005-12-22 03:26:15 as ** along with 3 people and 1 group Cortel shuns penka BioinfoCIPF
  • Protein structure prediction: inroads to biology.
    Mol Cell, Vol. 20, No. 6. (22 December 2005), pp. 811-819.
    by D Petrey, B Honig
    posted to bioinformatics folding protein_structure review structure_prediction by marcius to the group SGU-CIPF on 2005-12-22 00:53:03 as ** along with 3 people and 1 group vavi penka Haggan BioinfoCIPF
  • The relation between the divergence of sequence and structure in proteins.
    EMBO J, Vol. 5, No. 4. (April 1986), pp. 823-826.
    by C Chothia, AM Lesk
    posted to evolution structure structure_alignment structure_prediction by marcius to the group SGU-CIPF on 2005-12-20 00:56:52 as read along with 7 people and 5 groups ana pansapiens jwm Einat xdeupi ffranca insectopalo structural_bioinformatics Radiation_Damage Stressosome Bioinformatics BioinfoCIPF
  • Toward High-Resolution de Novo Structure Prediction for Small Proteins
    Science, Vol. 309, No. 5742. (16 September 2005), pp. 1868-1871.
    by Philip Bradley, Kira M Misura, David Baker
    posted to ab-initio biophysics computational_biology structure_prediction by marcius to the group SGU-CIPF on 2005-11-02 09:16:25 as read along with 8 people and 3 groups BragilMassoud ana barry thaliana jwm vavi gbart thamelry structural_bioinformatics Bioinformatics BioinfoCIPF
  • Progress in Modeling of Protein Structures and Interactions
    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 SGU-CIPF on 2005-10-28 00:14:41 as read along with 12 people and 1 group thaliana jwm vavi bicko KyuhoLee eweaver tny nickolay dgront rsantana mirzazadeh insectopalo BioinfoCIPF
  • Structure-derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds.
    J Mol Biol, Vol. 224, No. 3. (5 April 1992), pp. 725-732.
    by G Casari, MJ Sippl
    posted to computational_biology review statistical_potentials structure_prediction by marcius to the group SGU-CIPF on 2005-10-26 19:19:29 as ** along with 1 group BioinfoCIPF
  • Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures.
    J Comput Aided Mol Des, Vol. 7, No. 4. (August 1993), pp. 473-501.
    by MJ Sippl
    posted to computational_biology review statistical_potentials structure_prediction by marcius to the group SGU-CIPF on 2005-10-26 19:19:19 as read along with 3 people and 1 group dgront aengisch mcbla BioinfoCIPF
  • Knowledge-based potentials for proteins.
    Curr Opin Struct Biol, Vol. 5, No. 2. (April 1995), pp. 229-235.
    by MJ Sippl
    posted to computational_biology review statistical_potentials structure_prediction by marcius to the group SGU-CIPF on 2005-10-26 19:19:08 as ** along with 3 people and 1 group chad_davis eckart_bindewald tolot27 BioinfoCIPF
  • Threading thrills and threats.
    Structure, Vol. 4, No. 1. (15 January 1996), pp. 15-19.
    by MJ Sippl, H Flöckner
    posted to computational_biology review statistical_potentials structure_prediction by marcius to the group SGU-CIPF on 2005-10-26 19:18:59 as ** along with 1 group BioinfoCIPF
  • Empirical potentials and functions for protein folding and binding.
    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 SGU-CIPF on 2005-10-26 19:18:50 as ** along with 1 person and 1 group chad_davis BioinfoCIPF
  • Theory and simulation. Old problems, new paradigms.
    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 SGU-CIPF on 2005-10-26 19:18:40 as ** along with 1 group BioinfoCIPF
  • The role of protein structure in genomics.
    FEBS Lett, Vol. 476, No. 1-2. (30 June 2000), pp. 98-102.
    by FS Domingues, WA Koppensteiner, MJ Sippl
    posted to computational_biology review statistical_potentials structural_genomics structure_prediction by marcius to the group SGU-CIPF on 2005-10-26 19:18:29 as ** along with 1 group BioinfoCIPF
  • Knowledge-based potentials--back to the roots.
    Biochemistry (Mosc), Vol. 63, No. 3. (March 1998), pp. 247-252.
    by WA Koppensteiner, MJ Sippl
    posted to computational_biology review statistical_potentials structure_prediction by marcius to the group SGU-CIPF on 2005-10-26 19:18:16 as read along with 1 person and 1 group tolot27 BioinfoCIPF
  • Assessment of CASP6 predictions for new and nearly new fold targets.
    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 SGU-CIPF on 2005-10-22 09:12:32 as ** along with 1 person and 1 group nigham BioinfoCIPF
  • Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models.
    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 SGU-CIPF on 2005-10-22 09:12:12 as *** along with 2 people and 1 group nigham dgront BioinfoCIPF
  • Protein structure prediction in CASP6 using CHIMERA and FAMS.
    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 SGU-CIPF on 2005-10-22 09:11:43 as ** along with 1 group BioinfoCIPF
  • Protein structure prediction using a variety of profile libraries and 3D verification.
    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 SGU-CIPF on 2005-10-22 09:11:09 as ** along with 1 group BioinfoCIPF
  • SAM-T04: what's new in protein-structure prediction for CASP6.
    Proteins (26 September 2005)
    by Kevin Karplus, Sol Katzman, George Shackleford, Martina Koeva, Jenny Draper, Bret Barnes, Marcia Soriano, Richard Hughey
    posted to cafasp casp sequence_alignment structure_prediction by marcius to the group SGU-CIPF on 2005-10-22 09:10:38 as ** along with 1 group BioinfoCIPF
  • Protein loop structure prediction with flexible stem geometries.
    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 SGU-CIPF on 2005-10-22 09:06:47 as ** along with 1 person and 1 group vavi BioinfoCIPF
  • Assessment of predictions submitted for the CASP6 comparative modelling category.
    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 SGU-CIPF on 2005-10-22 08:59:31 as **** along with 3 people and 1 group nigham ffranca magia215 BioinfoCIPF
  • Free modeling with Rosetta in CASP6.
    Proteins (26 September 2005)
    by Philip Bradley, Lars Malmström, Bin Qian, 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 SGU-CIPF on 2005-10-22 08:58:20 as *** along with 4 people and 1 group jwm dgront schuylrp mirzazadeh BioinfoCIPF
  • Prediction of novel and analogous folds using fragment assembly and fold recognition.
    Proteins (26 September 2005)
    by D T T Jones, K Bryson, A Coleman, 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 SGU-CIPF on 2005-10-22 08:57:29 as **** along with 1 group BioinfoCIPF
  • SPARKS 2 and SP(3) servers in CASP 6.
    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 SGU-CIPF on 2005-10-22 08:56:27 as *** along with 1 person and 1 group j3xucite BioinfoCIPF
  • Progress over the first decade of CASP experiments.
    Proteins (26 September 2005)
    by Andriy Kryshtafovych, Ceslovas Venclovas, Krzysztof Fidelis, John Moult
    posted to casp review structure_prediction by marcius to the group SGU-CIPF on 2005-10-22 08:55:22 as ** along with 3 people and 1 group bicko ffranca schuylrp BioinfoCIPF
  • Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation.
    Proc Natl Acad Sci U S A, Vol. 101, No. 43. (26 October 2004), pp. 15346-15351.
    by B Qian, AR Ortiz, D Baker
    posted to biophysics clustering comparative_modeling protein_structure structure_prediction by marcius to the group SGU-CIPF on 2005-10-22 05:00:32 as **** along with 4 people and 3 groups ana barry lna dgront structural_bioinformatics Bioinformatics BioinfoCIPF
  • Have we seen all structures corresponding to short protein fragments in the Protein Data Bank? An update.
    Protein Eng, Vol. 16, No. 6. (June 2003), pp. 407-414.
    by P Du, M Andrec, RM Levy
    posted to protein_fragments structure_prediction by marcius to the group SGU-CIPF on 2005-10-22 03:09:41 as ** along with 1 group BioinfoCIPF
  • Structure prediction of membrane proteins.
    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 SGU-CIPF on 2005-10-22 03:09:41 as ** along with 1 group BioinfoCIPF
  • State-of-the-art in membrane protein prediction.
    Appl Bioinformatics, Vol. 1, No. 1. (2002), pp. 21-35.
    by CP Chen, B Rost
    posted to membrane_protein protein_structure review structure_prediction by marcius to the group SGU-CIPF on 2005-10-22 03:09:41 as ** along with 1 group BioinfoCIPF
  • Hamiltonians for protein tertiary structure prediction based on three-dimensional environment principles.
    J Mol Biol, Vol. 233, No. 3. (October 1993), pp. 480-487.
    by T Madej, MC Mossing
    posted to algorithms computational_biology protein_structure structure_prediction by marcius to the group SGU-CIPF on 2005-10-22 03:09:41 as ** along with 1 group BioinfoCIPF
  • Computational analysis of alpha-helical membrane protein structure: implications for the prediction of 3D structural models.
    Protein Eng Des Sel, Vol. 17, No. 8. (August 2004), pp. 613-624.
    by TA Eyre, L Partridge, JM Thornton
    posted to computational_biology membrane_protein protein_structure structure_prediction by marcius to the group SGU-CIPF on 2005-10-22 03:09:41 as ** along with 1 group BioinfoCIPF
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