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Group: BioinfoCIPF - with tag computational_biology [53 articles]

グループ BioinfoCIPF のメンバーが最近追加した論文の一覧 with tag computational_biology
  • Sampling Realistic Protein Conformations Using Local Structural Bias
    PLoS Computational Biology, Vol. 2, No. 9. (1 September 2006), e131.
    by Thomas Hamelryck, John T Kent, Anders Krogh
    posted to biophysics clustering computational_biology dynamics structure by marcius to the group BioinfoCIPF on 2006-09-29 08:57:03 as ** along with 1 person and 1 group mijam SGU-CIPF
  • Physical Origins of Protein Superfamilies.
    J Mol Biol (6 February 2006)
    by Konstantin B B Zeldovich, Igor N N Berezovsky, Eugene I I Shakhnovich
    posted to biophysics computational_biology evolution protein structure by marcius to the group BioinfoCIPF on 2006-04-27 20:29:04 as ** along with 3 people and 2 groups Einat laurabailey happy_manatee structural_bioinformatics SGU-CIPF
  • Predicting free energy landscapes for complexes of double-stranded chain molecules
    The Journal of Chemical Physics, Vol. 114, No. 9. (2001), pp. 4253-4266.
    by Wenbing Zhang, Shi J Chen
    posted to biophysics computational_biology dna folding rna by marcius to the group BioinfoCIPF on 2006-04-21 22:11:14 as ** along with 1 person and 2 groups condon beta SGU-CIPF
  • Theory for the conformational changes of double-stranded chain molecules
    The Journal of Chemical Physics, Vol. 109, No. 11. (1998), pp. 4602-4616.
    by Shi J Chen, Ken A Dill
    posted to biophysics computational_biology dna folding rna by marcius to the group BioinfoCIPF on 2006-04-21 22:11:01 as ** along with 1 person and 2 groups condon beta SGU-CIPF
  • Statistical thermodynamics of double-stranded polymer molecules
    The Journal of Chemical Physics, Vol. 103, No. 13. (1995), pp. 5802-5813.
    by Shi J Chen, Ken A Dill
    posted to biophysics computational_biology dna folding rna by marcius to the group BioinfoCIPF on 2006-04-21 22:10:14 as ** along with 1 person and 2 groups condon beta SGU-CIPF
  • 2020 ComputingCan computers help to explain biology?
    Nature, Vol. 440, No. 7083. (22 March 2006), pp. 416-417.
    by Roger Brent, Jehoshua Bruck
    posted to computational_biology views by marcius to the group BioinfoCIPF on 2006-03-28 06:30:11 as ** along with 5 people and 1 group cmmorel eweaver ddahlem dullhunk bigbossman SGU-CIPF
  • Evidence that miRNAs are different from other RNAs.
    Cell Mol Life Sci, Vol. 63, No. 2. (January 2006), pp. 246-254.
    by BH Zhang, XP Pan, SB Cox, GP Cobb, TA Anderson
    posted to biophysics computational_biology microrna by marcius to the group BioinfoCIPF on 2006-03-17 18:48:36 as ** along with 4 people and 5 groups eckart_bindewald andersbj dchughes cdawson microRNA G4ID SGU-CIPF GIG Genetics-of-Gambling
  • Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency
    RNA, Vol. 11, No. 5. (1 May 2005), pp. 578-591.
    by Peter Clote, Fabrizio Ferre, Evangelos Kranakis, Danny Krizanc
    posted to computational_biology folding rna by marcius to the group BioinfoCIPF on 2006-03-17 07:35:58 as ** along with 2 people and 1 group arcticrasta elfar SGU-CIPF
  • Computer-aided NMR assay for detecting natively folded structural domains.
    Protein Sci (7 March 2006)
    by Takayuki Hondoh, Atsushi Kato, Shigeyuki Yokoyama, Yutaka Kuroda
    posted to computational_biology nmr protein_domains by marcius to the group BioinfoCIPF on 2006-03-15 23:01:54 as ** along with 1 group SGU-CIPF
  • 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 BioinfoCIPF on 2006-03-15 22:59:20 as ** along with 1 person and 1 group thaliana SGU-CIPF
  • Long- and short-range interactions in native protein structures are consistent/minimally frustrated in sequence space.
    Proteins, Vol. 50, No. 1. (1 January 2003), pp. 35-43.
    by S Miyazawa, RL Jernigan
    posted to computational_biology model_assessment statistical_potentials by marcius to the group BioinfoCIPF on 2006-03-07 18:44:30 as ** along with 1 person and 3 groups ana structural_bioinformatics Bioinformatics SGU-CIPF
  • Predicting candidate genomic sequences that correspond to synthetic functional RNA motifs.
    Nucleic Acids Res, Vol. 33, No. 18. (2005), pp. 6057-6069.
    by U Laserson, HH Gan, T Schlick
    posted to computational_biology function genome ncrna rna by marcius to the group BioinfoCIPF on 2006-03-06 22:49:02 as ** along with 1 group SGU-CIPF
  • Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes
    Nature Biotechnology, Vol. 23, No. 11. (23 October 2005), pp. 1424-1433.
    by Robert Penchovsky, Ronald R Breaker
    posted to computational_biology ncrna by marcius to the group BioinfoCIPF on 2006-03-06 22:33:55 as ** along with 3 people and 1 group rklancer dbikard austin SGU-CIPF
  • RNAshapes: an integrated RNA analysis package based on abstract shapes
    Bioinformatics, Vol. 22, No. 4. (15 February 2006), pp. 500-503.
    by Peter Steffen, Bjorn Vosharp, Marc Rehmsmeier, Jens Reeder, Robert Giegerich
    posted to bioinformatics computational_biology rna secondary_structure by marcius to the group BioinfoCIPF on 2006-02-16 18:13:15 as ** along with 2 people and 1 group penka Hosna SGU-CIPF
  • Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets.
    Cell, Vol. 120, No. 1. (14 January 2005), pp. 15-20.
    by BP Lewis, CB Burge, DP Bartel
    posted to bioinformatics computational_biology microrna ncrna by marcius to the group BioinfoCIPF on 2006-02-13 20:24:00 as ** along with 10 people and 2 groups jfr maryee eckart_bindewald tardigrade mortenlindow andersbj mtagaya heliopais Alexander_Kanitz elfar microRNA SGU-CIPF
  • 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 BioinfoCIPF on 2006-02-11 01:12:07 as ** along with 1 person and 1 group eckart_bindewald SGU-CIPF
  • Computational genomics of noncoding RNA genes.
    Cell, Vol. 109, No. 2. (19 April 2002), pp. 137-140.
    by SR Eddy
    posted to computational_biology microrna review by marcius to the group BioinfoCIPF on 2006-02-10 21:09:57 as ** along with 1 person and 1 group arcticrasta SGU-CIPF
  • Computational identification of noncoding RNAs in E. coli by comparative genomics.
    Curr Biol, Vol. 11, No. 17. (4 September 2001), pp. 1369-1373.
    by E Rivas, RJ Klein, TA Jones, SR Eddy
    posted to computational_biology genes genome rna by marcius to the group BioinfoCIPF on 2006-02-10 20:26:44 as ** along with 5 people and 3 groups evaf eckart_bindewald arcticrasta dquest bsmagic Bioinformatics bioinplant SGU-CIPF
  • 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 BioinfoCIPF on 2006-01-27 01:13:40 as ** along with 1 group SGU-CIPF
  • Database-derived potentials dependent on protein size for in silico folding and design.
    Biophys J, Vol. 87, No. 1. (July 2004), pp. 171-181.
    by Y Dehouck, D Gilis, M Rooman
    posted to computational_biology model_assessment by marcius to the group BioinfoCIPF on 2006-01-20 22:59:04 as ** along with 1 group SGU-CIPF
  • An Information Theoretic Approach to Macromolecular Modeling: II. Force Fields.
    Biophys J, Vol. 89, No. 5. (November 2005), pp. 3008-3016.
    by T Aynechi, ID Kuntz
    posted to bioinformatics biophysics computational_biology model_assessment molecular_dynamics by marcius to the group BioinfoCIPF on 2006-01-20 22:54:26 as ** along with 1 person and 1 group nickolay SGU-CIPF
  • Simulation of non-specific proteinmRNA interactions
    Nucleic Acids Research, Vol. 33, No. 21. (2005), pp. 6694-6699.
    by James Magee, Jim Warwicker
    posted to biophysics computational_biology molecular_dynamics protein rna by marcius to the group BioinfoCIPF on 2006-01-12 19:13:27 as ** along with 1 group SGU-CIPF
  • A comprehensive comparison of comparative RNA structure prediction approaches.
    BMC Bioinformatics, Vol. 5, No. 1. (30 September 2004)
    by PP Gardner, R Giegerich
    posted to bioinformatics computational_biology rna secondary_structure structure by marcius to the group BioinfoCIPF on 2005-12-21 19:13:13 as ** along with 7 people and 2 groups evaf austin andersbj arcticrasta penka Hosna Carnegie microRNA SGU-CIPF
  • RNA folding: models and perspectives.
    Curr Opin Struct Biol, Vol. 13, No. 3. (June 2003), pp. 309-316.
    by TR Sosnick, T Pan
    posted to biophysics computational_biology folding rna structure by marcius to the group BioinfoCIPF on 2005-12-20 01:07:48 as ** along with 3 people and 1 group evaf Hosna austin SGU-CIPF
  • 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 BioinfoCIPF 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 SGU-CIPF
  • 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 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.
    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 BioinfoCIPF on 2005-10-26 19:19:19 as read along with 3 people and 1 group dgront aengisch mcbla SGU-CIPF
  • 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 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.
    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 BioinfoCIPF on 2005-10-26 19:18:59 as ** along with 1 group SGU-CIPF
  • 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 BioinfoCIPF on 2005-10-26 19:18:50 as ** along with 1 person and 1 group chad_davis SGU-CIPF
  • 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 BioinfoCIPF on 2005-10-26 19:18:40 as ** along with 1 group SGU-CIPF
  • 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 BioinfoCIPF on 2005-10-26 19:18:29 as ** along with 1 group SGU-CIPF
  • 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 BioinfoCIPF on 2005-10-26 19:18:16 as read along with 1 person and 1 group tolot27 SGU-CIPF
  • Convergent evolution as a mechanism for pathogenic adaptation.
    Trends Microbiol (7 September 2005)
    by Sergey Sikora, Alex Strongin, Adam Godzik
    posted to comparative_modeling computational_biology evolution molecular_mimicry by marcius to the group BioinfoCIPF on 2005-10-26 04:17:30 as ** along with 1 person and 3 groups ana structural_bioinformatics Bioinformatics SGU-CIPF
  • How do side chains orient globally in protein structures?
    Proteins: Structure, Function, and Bioinformatics, Vol. 61, No. 3. (8 September 2005), pp. 513-522.
    by Aimin Yan, Robert L Jernigan
    posted to classification computational_biology protein_structure side_chains by marcius to the group BioinfoCIPF on 2005-10-23 02:54:16 as ** along with 2 people and 1 group aqeel blackbart SGU-CIPF
  • Comparative molecular dynamics-Similar folds and similar motions?
    Proteins (17 October 2005)
    by Andrew Pang, Yalini Arinaminpathy, Mark S P S Sansom, Philip C C Biggin
    posted to biophysics computational_biology molecular_dynamics protein_structure by marcius to the group BioinfoCIPF on 2005-10-22 16:56:55 as **** along with 1 group SGU-CIPF
  • 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 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.
    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 BioinfoCIPF on 2005-10-22 03:09:41 as ** along with 1 group SGU-CIPF
  • Recoverable one-dimensional encoding of protein three-dimensional structures.
    Bioinformatics (February 2005)
    by Akira RR Kinjo, Ken Nishikawa
    posted to structure_prediction computational_biology protein_structure by marcius to the group BioinfoCIPF on 2005-10-22 03:09:41 as ** along with 1 group SGU-CIPF
  • LGA: A method for finding 3D similarities in protein structures.
    Nucleic Acids Res, Vol. 31, No. 13. (July 2003), pp. 3370-3374.
    by A Zemla
    posted to algorithms computational_biology protein_structure structure_prediction by marcius to the group BioinfoCIPF on 2005-10-22 03:09:40 as ** along with 1 group SGU-CIPF
  • The grail problem.
    Genome Biol, Vol. 1, No. 1. (2000)
    by GA Petsko
    posted to computational_biology protein_structure structure_prediction by marcius to the group BioinfoCIPF on 2005-10-22 03:09:40 as ** along with 1 group SGU-CIPF
  • Model behavior.
    Genome Biol, Vol. 2, No. 7. (2001)
    by GA Petsko
    posted to computational_biology protein_structure structure_prediction by marcius to the group BioinfoCIPF on 2005-10-22 03:09:40 as ** along with 1 group SGU-CIPF
  • The protein structure prediction problem could be solved using the current PDB library.
    Proc Natl Acad Sci U S A, Vol. 102, No. 4. (25 January 2005), pp. 1029-1034.
    by Y Zhang, J Skolnick
    posted to computational_biology evolution protein_folding protein_structure structural_genomics by marcius to the group BioinfoCIPF on 2005-10-21 21:56:14 as read along with 9 people and 2 groups karbak iakes vavi alexg j3xucite kracher schuylrp jfmuggs neils Immunoinformatics SGU-CIPF
  • Scoring function for automated assessment of protein structure template quality
    Proteins: Structure, Function, and Bioinformatics, Vol. 57, No. 4., pp. 702-710.
    by Yang Zhang, Jeffrey Skolnick
    posted to computational_biology model_assessment protein_structure by marcius to the group BioinfoCIPF on 2005-10-21 21:55:27 as * along with 5 people and 1 group karbak dgront aengisch rabio granujilla SGU-CIPF
  • Discrimination of native loop conformations in membrane proteins: decoy library design and evaluation of effective energy scoring functions.
    Proteins, Vol. 52, No. 4. (1 September 2003), pp. 492-509.
    by LR Forrest, TB Woolf
    posted to computational_biology model_assessment protein_structure software by marcius to the group BioinfoCIPF on 2005-10-21 21:08:44 as * along with 1 person and 1 group thaliana SGU-CIPF
  • Effective energy function for proteins in solution.
    Proteins, Vol. 35, No. 2. (1 May 1999), pp. 133-152.
    by T Lazaridis, M Karplus
    posted to computational_biology model_assessment protein_folding software by marcius to the group BioinfoCIPF on 2005-10-21 21:08:08 as *** along with 4 people and 1 group bluvsh1 choonpeng hmk kgutwin SGU-CIPF
  • Ab initio folding of proteins using restraints derived from evolutionary information.
    Proteins, Vol. Suppl 3 (1999), pp. 177-185.
    by AR Ortiz, A Kolinski, P Rotkiewicz, B Ilkowski, J Skolnick
    posted to biophysics computational_biology evolution protein_folding by marcius to the group BioinfoCIPF on 2005-10-21 20:28:33 as ** along with 1 person and 1 group gbart SGU-CIPF
  • Sequence evolution and the mechanism of protein folding.
    Biophys J, Vol. 79, No. 4. (October 2000), pp. 1787-1799.
    by AR Ortiz, J Skolnick
    posted to biophysics computational_biology evolution protein_structure by marcius to the group BioinfoCIPF on 2005-10-21 20:27:05 as read along with 2 people and 1 group penka cjeans SGU-CIPF
  • MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading.
    Proteins, Vol. 49, No. 3. (15 November 2002), pp. 350-364.
    by L Lu, H Lu, J Skolnick
    posted to computational_biology protein_interactions protein_structure by marcius to the group BioinfoCIPF on 2005-10-21 19:36:56 as *** along with 6 people and 4 groups ana bicko chad_davis sangeetha ruvido kgutwin structural_bioinformatics Bioinformatics insilicodrug SGU-CIPF
  • The PDB is a covering set of small protein structures.
    J Mol Biol, Vol. 334, No. 4. (5 December 2003), pp. 793-802.
    by D Kihara, J Skolnick
    posted to computational_biology evolution protein_fragments protein_structure structural_genomics by marcius to the group BioinfoCIPF on 2005-10-21 10:08:41 as read along with 2 people and 1 group iakes j3xucite SGU-CIPF
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