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marcius's protein_structure [86 articles]

Recent papers added to marcius's library classified by the tag protein_structure. You can also see everyone's protein_structure.
  • From The Cover: Global mapping of the protein structure space and application in structure-based inference of protein function
    PNAS, Vol. 102, No. 10. (8 March 2005), pp. 3651-3656.
    by Jingtong Hou, Se-Ran Jun, Chao Zhang, Sung-Hou Kim
    posted to algorithms bioinformatics clustering protein_structure by marcius on 2006-10-26 08:42:48 as ** along with 1 person and 2 groups tny BioinfoCIPF SGU-CIPF
  • Recent advances in the development and application of implicit solvent models in biomolecule simulations.
    Curr Opin Struct Biol, Vol. 14, No. 2. (April 2004), pp. 217-224.
    by M Feig, CL Brooks
    posted to biophysics foce_field folding protein_structure review by marcius on 2006-10-02 10:50:01 as ** along with 5 people and 2 groups apostola simone ttjoseph gane5h RamuAnandakrishnan BioinfoCIPF SGU-CIPF
  • Effective energy functions for protein structure prediction.
    Curr Opin Struct Biol, Vol. 10, No. 2. (April 2000), pp. 139-145.
    by T Lazaridis, M Karplus
    posted to biophysics foce_field folding protein_structure review by marcius on 2006-10-02 10:49:24 as ** along with 2 people and 2 groups karbak nigham BioinfoCIPF SGU-CIPF
  • Empirical force fields for biological macromolecules: Overview and issues
    Journal of Computational Chemistry, Vol. 25, No. 13. (1 July 2004), pp. 1584-1604.
    by Alexander D Mackerell
    posted to biophysics foce_field folding protein_structure review by marcius on 2006-10-02 10:47:07 as ** along with 5 people and 2 groups BragilMassoud dgront loison mirzazadeh AndreaColetta BioinfoCIPF SGU-CIPF
  • Force fields for protein simulations.
    Adv Protein Chem, Vol. 66 (2003), pp. 27-85.
    by JW Ponder, DA Case
    posted to biophysics foce_field folding protein_structure review by marcius on 2006-10-02 10:46:40 as ** along with 3 people and 2 groups karbak papatonyhill hmk BioinfoCIPF SGU-CIPF
  • Thermodynamics of protein folding: a microscopic view.
    Biophys Chem, Vol. 100, No. 1-3. (2003), pp. 367-395.
    by T Lazaridis, M Karplus
    posted to biophysics foce_field folding protein_structure review by marcius on 2006-10-02 10:46:31 as ** along with 1 person and 2 groups karbak BioinfoCIPF SGU-CIPF
  • Choosing SNPs Using Feature Selection.
    Proc IEEE Comput Syst Bioinform Conf (2005), pp. 301-309.
    by TM Phuong, Z Lin, RB Altman
    posted to function prediction protein_structure snp by marcius on 2006-09-07 17:40:06 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • Structural characterization of proteins using residue environments.
    Proteins, Vol. 61, No. 4. (1 December 2005), pp. 741-747.
    by SD Mooney, MH Liang, R DeConde, RB Altman
    posted to function prediction protein_structure by marcius on 2006-09-07 17:39:29 as ** along with 1 person and 2 groups nickolay BioinfoCIPF SGU-CIPF
  • Assigning new GO annotations to protein data bank sequences by combining structure and sequence homology.
    Proteins, Vol. 58, No. 4. (1 March 2005), pp. 855-865.
    by JV Ponomarenko, PE Bourne, IN Shindyalov
    posted to bioinformatics evolution protein_function protein_structure by marcius on 2006-09-07 17:24:49 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • The RCSB PDB information portal for structural genomics.
    Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006)
    by A Kouranov, L Xie, J de la Cruz, L Chen, J Westbrook, PE Bourne, HM Berman
    posted to databases protein_structure structural_genomics by marcius on 2006-09-07 17:21:33 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • Crystal structure of TM1367 from Thermotoga maritima at 1.90 A resolution reveals an atypical member of the cyclophilin (peptidylprolyl isomerase) fold.
    Proteins, Vol. 63, No. 4. (1 June 2006), pp. 1112-1118.
    by KK Jin, SS Krishna, R Schwarzenbacher, D McMullan, P Abdubek, S Agarwalla, E Ambing, H Axelrod, JM Canaves, HJ Chiu, AM Deacon, M DiDonato, MA Elsliger, J Feuerhelm, A Godzik, C Grittini, SK Grzechnik, J Hale, E Hampton, J Haugen, M Hornsby, L Jaroszewski, HE Klock, MW Knuth, E Koesema, A Kreusch, P Kuhn, SA Lesley, MD Miller, K Moy, E Nigoghossian, L Okach, S Oommachen, J Paulsen, K Quijano, R Reyes, C Rife, RC Stevens, G Spraggon, H van den Bedem, J Velasquez, A White, G Wolf, GW Han, Q Xu, KO Hodgson, J Wooley, IA Wilson
    posted to protein_structure by marcius on 2006-09-07 17:14:18 as ** along with 1 person and 2 groups JCSGpublications BioinfoCIPF SGU-CIPF
  • Crystal structure of a glycerate kinase (TM1585) from Thermotoga maritima at 2.70 A resolution reveals a new fold.
    Proteins, Vol. 65, No. 1. (1 October 2006), pp. 243-248.
    by R Schwarzenbacher, D McMullan, SS Krishna, Q Xu, MD Miller, JM Canaves, MA Elsliger, R Floyd, SK Grzechnik, L Jaroszewski, HE Klock, E Koesema, JS Kovarik, A Kreusch, P Kuhn, TM McPhillips, AT Morse, K Quijano, G Spraggon, RC Stevens, H van den Bedem, G Wolf, KO Hodgson, J Wooley, AM Deacon, A Godzik, SA Lesley, IA Wilson
    posted to protein_structure by marcius on 2006-09-07 17:12:58 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • Structural biologyProteins downhill all the way
    Nature, Vol. 442, No. 7100. (19 July 2006), pp. 255-256.
    by Jeffery W Kelly
    posted to biophysics folding news protein_structure views by marcius on 2006-07-20 10:06:15 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • Atom-by-atom analysis of global downhill protein folding
    Nature, Vol. 442, No. 7100. (14 June 2006), pp. 317-321.
    by Mourad Sadqi, David Fushman, Victor Muñoz
    posted to biophysics folding protein_structure by marcius on 2006-07-20 10:05:38 as ** along with 4 people and 2 groups wouterboomsma choonpeng gisle huyun110 BioinfoCIPF SGU-CIPF
  • How different amino acid sequences determine similar protein structures: The structure and evolutionary dynamics of the globins
    Journal of Molecular Biology, Vol. 136, No. 3. (25 January 1980), pp. 225-230.
    by Arthur M Lesk, Cyrus Chothia
    posted to biophysics comparative_modeling evolution protein_structure by marcius on 2006-04-30 01:12:36 as ** along with 2 people and 4 groups ana barry structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
  • PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics.
    BMC Bioinformatics, Vol. 7, No. 1. (6 February 2006)
    by Marcin von Grotthuss, Dariusz Plewczynski, Krzysztof Ginalski, Leszek Rychlewski, Eugene I Shakhnovich
    posted to bioinformatics databases protein_function protein_structure by marcius on 2006-02-27 20:16:54 as ** along with 2 people and 3 groups caporaso sim82 biomedical-nlp BioinfoCIPF SGU-CIPF
  • 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 on 2006-02-07 02:17:31 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • 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 on 2006-02-02 05:48:58 as ** along with 2 people and 2 groups chad_davis ffranca BioinfoCIPF SGU-CIPF
  • Residue-rotamer-reduction algorithm for the protein side-chain conformation problem
    Bioinformatics, Vol. 22, No. 2. (15 January 2006), pp. 188-194.
    by Wei Xie, Nikolaos V Sahinidis
    posted to ab-initio biophysics protein_structure rotamers by marcius on 2006-02-02 05:47:25 as ** along with 3 people and 2 groups bicko bluvsh1 carlk BioinfoCIPF SGU-CIPF
  • 'Protein Peeling': an approach for splitting a 3D protein structure into compact fragments
    Bioinformatics, Vol. 22, No. 2. (15 January 2006), pp. 129-133.
    by Jean-Christophe Gelly, Alexandre G de Brevern, Serge Hazout
    posted to algorithms bioinformatics protein_fragments protein_structure by marcius on 2006-02-02 05:44:16 as ** along with 7 people and 4 groups MarcoAlvarez ana barry dimka ttjoseph nickolay choonpeng structural_bioinformatics Bioinformatics BioinfoCIPF 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 on 2006-01-27 01:13:40 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • Knowledge-based potential functions in protein design.
    Curr Opin Struct Biol, Vol. 12, No. 4. (August 2002), pp. 447-452.
    by WP Russ, R Ranganathan
    posted to biophysics model_assessment protein_structure review by marcius on 2006-01-20 23:02:36 as ** along with 1 person and 2 groups gbart BioinfoCIPF SGU-CIPF
  • Prediction of protein thermostability with a direction- and distance-dependent knowledge-based potential.
    Protein Sci, Vol. 14, No. 10. (October 2005), pp. 2682-2692.
    by C Hoppe, D Schomburg
    posted to model_assessment protein_structure protein_threading by marcius on 2006-01-19 19:51:53 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • PMUT: a web-based tool for the annotation of pathological mutations on proteins.
    Bioinformatics, Vol. 21, No. 14. (15 July 2005), pp. 3176-3178.
    by C Ferrer-Costa, JL Gelpí, L Zamakola, I Parraga, X de la Cruz, M Orozco
    posted to protein protein_structure servers snp by marcius on 2006-01-17 19:14:25 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • Characterization of disease-associated single amino acid polymorphisms in terms of sequence and structure properties.
    J Mol Biol, Vol. 315, No. 4. (25 January 2002), pp. 771-786.
    by C Ferrer-Costa, M Orozco, X de la Cruz
    posted to bioinformatics classification protein protein_structure snp by marcius on 2006-01-17 19:13:45 as ** along with 1 person and 3 groups caporaso biomedical-nlp BioinfoCIPF SGU-CIPF
  • 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 on 2006-01-13 23:58:03 as ** along with 1 person and 2 groups miguel BioinfoCIPF SGU-CIPF
  • Evolutionary information for specifying a protein fold
    Nature, Vol. 437, No. 7058., pp. 512-518.
    by Michael Socolich, Steve W Lockless, William P Russ, Heather Lee, Kevin H Gardner, Rama Ranganathan
    posted to bioinformatics protein_folding protein_structure software by marcius on 2005-12-28 14:04:37 as ** along with 14 people and 5 groups ana barry lna bpb Einat balajis gbart analogAI nirfriedman caporaso massivemayhem mingzhi bethbromley ca3295 structural_bioinformatics Bioinformatics biomedical-nlp BioinfoCIPF SGU-CIPF
  • The evolution of protein structures.
    Cold Spring Harb Symp Quant Biol, Vol. 52 (1987), pp. 399-405.
    by C Chothia, AM Lesk
    posted to classification evolution protein_structure by marcius on 2005-12-28 11:49:42 as ** along with 1 person and 2 groups penka BioinfoCIPF SGU-CIPF
  • A tour of structural genomics.
    Nat Rev Genet, Vol. 2, No. 10. (October 2001), pp. 801-809.
    by SE Brenner
    posted to protein_structure review structural_genomics by marcius on 2005-12-22 06:50:22 as ** along with 1 person and 2 groups penka BioinfoCIPF SGU-CIPF
  • 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 on 2005-12-22 00:53:03 as ** along with 3 people and 2 groups vavi penka Haggan BioinfoCIPF SGU-CIPF
  • Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design.
    Nucleic Acids Res, Vol. 33, No. 18. (2005), pp. 5861-5867.
    by Gong Cheng, Bin Qian, Ram Samudrala, David Baker
    posted to biophysics evolution protein_function protein_structure by marcius on 2005-11-02 09:14:59 as ** along with 6 people and 3 groups bicko Einat alexg nickolay sriram_s ladab structural_bioinformatics BioinfoCIPF SGU-CIPF
  • Structural similarity to bridge sequence space: finding new families on the bridges.
    Protein Sci, Vol. 14, No. 5. (May 2005), pp. 1305-1314.
    by PK Shah, P Aloy, P Bork, RB Russell
    posted to bioinformatics classification clustering protein_structure structural_genomics by marcius on 2005-10-28 19:11:21 as *** along with 2 people and 2 groups eweaver drastic BioinfoCIPF SGU-CIPF
  • Fragnostic: walking through protein structure space.
    Nucleic Acids Res, Vol. 33, No. Web Server issue. (1 July 2005)
    by I Friedberg, A Godzik
    posted to bioinformatics classification clustering protein_fragments protein_structure by marcius on 2005-10-23 09:49:10 as read along with 7 people and 4 groups ana barry pansapiens aalibes Einat alexg eweaver structural_bioinformatics Bioinformatics BioinfoCIPF 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 on 2005-10-23 02:54:16 as ** along with 2 people and 2 groups aqeel blackbart BioinfoCIPF 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 on 2005-10-22 16:56:55 as **** along with 1 person and 2 groups ubcg08l BioinfoCIPF SGU-CIPF
  • 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 on 2005-10-22 09:06:47 as ** along with 1 person and 2 groups vavi BioinfoCIPF SGU-CIPF
  • 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 on 2005-10-22 08:59:31 as **** along with 3 people and 2 groups nigham ffranca magia215 BioinfoCIPF SGU-CIPF
  • 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 on 2005-10-22 08:57:29 as **** along with 2 groups BioinfoCIPF SGU-CIPF
  • 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 on 2005-10-22 08:56:27 as *** along with 1 person and 2 groups j3xucite BioinfoCIPF SGU-CIPF
  • Evaluating the usefulness of protein structure models for molecular replacement.
    Bioinformatics, Vol. 21, No. suppl_2. (1 September 2005)
    by Alejandro Giorgetti, Domenico Raimondo, Adriana Erica E Miele, Anna Tramontano
    posted to comparative_modeling protein_structure by marcius on 2005-10-22 08:54:54 as ** along with 1 person and 2 groups ffranca BioinfoCIPF SGU-CIPF
  • 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 on 2005-10-22 05:00:32 as **** along with 4 people and 4 groups ana barry lna dgront structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
  • 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 on 2005-10-22 03:09:41 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • 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 on 2005-10-22 03:09:41 as ** along with 2 groups BioinfoCIPF 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 on 2005-10-22 03:09:41 as ** along with 2 groups BioinfoCIPF 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 on 2005-10-22 03:09:41 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • Assembly of a polytopic membrane protein structure from the solution structures of overlapping peptide fragments of bacteriorhodopsin.
    Biophys J, Vol. 81, No. 2. (August 2001), pp. 1029-1036.
    by M Katragadda, JL Alderfer, PL Yeagle
    posted to membrane_protein protein_structure structure_prediction by marcius on 2005-10-22 03:09:41 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • Protein complexes: structure prediction challenges for the 21(st) century.
    Curr Opin Struct Biol, Vol. 15, No. 1. (February 2005), pp. 15-22.
    by P Aloy, M Pichaud, RB Russell
    posted to protein_complexes protein_structure review structure_prediction by marcius on 2005-10-22 03:09:41 as ** along with 2 groups BioinfoCIPF 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 on 2005-10-22 03:09:41 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • PROTEIN REFINEMENT: A NEW CHALLENGE FOR CASP IN ITS 10TH ANNIVERSARY
    Bioinformatics, Vol. 21, No. 3. (February 2005), 277.
    by Alfonso Valencia
    posted to casp protein_structure structure_prediction by marcius on 2005-10-22 03:09:41 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • Empirical limits for template-based protein structure prediction: the CASP5 example.
    FEBS Lett, Vol. 579, No. 5. (February 2005), pp. 1203-1207.
    by Contreras B Moreira, I Ezkurdia, ML Tress, A Valencia
    posted to casp protein_structure structure_prediction by marcius on 2005-10-22 03:09:41 as ** along with 2 groups BioinfoCIPF SGU-CIPF
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