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analogAIs protein-structure [45 articles]

Neue Publikationen in analogAIs Bibliothek eingetragen unter dem Bezeichner: protein-structure. You can also see everyone's protein-structure.
  • Finding the fittest fold: using the evolutionary record to design new proteins.
    Cell, Vol. 122, No. 6. (23 September 2005), pp. 832-834.
    by RG Smock, LM Gierasch
    posted to caig protein-structure proteinfolding residue-covariation by analogAI on 2006-07-05 08:27:59 as read along with 2 people and 3 groups marcius caporaso biomedical-nlp BioinfoCIPF SGU-CIPF
  • Stability improvement of antibodies for extracellular and intracellular applications: CDR grafting to stable frameworks and structure-based framework engineering.
    Methods, Vol. 34, No. 2. (October 2004), pp. 184-199.
    by S Ewert, A Honegger, A Plückthun
    posted to cdr immunoglobulin protein-engineering protein-stability protein-structure residue-covariation review-article by analogAI on 2006-06-03 07:07:31 as **
  • notes Protein secondary structure: entropy, correlations and prediction.
    Bioinformatics, Vol. 20, No. 10. (10 July 2004), pp. 1603-1611.
    by GE Crooks, SE Brenner
    posted to informationtheory protein-structure residue-covariation by analogAI on 2006-05-05 20:58:37 as read along with 2 people and 1 group Einat leelarcombe structural_bioinformatics
  • Improving contact predictions by the combination of correlated mutations and other sources of sequence information.
    Fold Des, Vol. 2, No. 3. (1997)
    by O Olmea, A Valencia
    posted to protein-structure residue-covariation by analogAI on 2006-05-05 05:31:43 as **
  • notes A graphical interface for correlated mutations and other protein structure prediction methods.
    Comput Appl Biosci, Vol. 13, No. 3. (June 1997), pp. 319-321.
    by F Pazos, O Olmea, A Valencia
    posted to protein-structure residue-covariation by analogAI on 2006-05-05 05:18:52 as read
  • Native protein sequences are close to optimal for their structures.
    Proc Natl Acad Sci U S A, Vol. 97, No. 19. (12 September 2000), pp. 10383-10388.
    by B Kuhlman, D Baker
    posted to protein-structure residue-covariation by analogAI on 2006-05-05 04:56:03 as read along with 2 people jwm gisle
  • Stabilization centers in proteins: identification, characterization and predictions.
    J Mol Biol, Vol. 272, No. 4. (3 October 1997), pp. 597-612.
    by Z Dosztányi, A Fiser, I Simon
    posted to protein-stability protein-structure residue-covariation by analogAI on 2005-12-21 05:55:53 as **** along with 1 person and 1 group Einat structural_bioinformatics
  • Simulating protein evolution in sequence and structure space.
    Curr Opin Struct Biol, Vol. 14, No. 2. (April 2004), pp. 202-207.
    by Y Xia, M Levitt
    posted to computer-simulation protein-sequence protein-structure proteinfolding by analogAI on 2005-12-21 05:11:20 as **** along with 10 people and 4 groups betainverse korakot mdimmic karbak rmj001 ana barry aalibes gbart insectopalo Philosophy_of_Information Blog_and_Wiki_Research structural_bioinformatics Bioinformatics
  • The identification of conserved interactions within the SH3 domain by alignment of sequences and structures.
    Protein Sci, Vol. 9, No. 11. (November 2000), pp. 2170-2180.
    by SM Larson, AR Davidson
    posted to protein-structure residue-covariation by analogAI on 2005-12-21 03:57:38 as *****
  • 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 protein-structure residue-covariation by analogAI on 2005-12-21 03:52:53 as ***** along with 15 people and 3 groups ca3295 lna dimka marcius eckart_bindewald gbart nirfriedman dgront caporaso choonpeng efge carlescorbi mingzhi yalexeev weisblum biomedical-nlp BioinfoCIPF SGU-CIPF
  • Analysis of covariation in an SH3 domain sequence alignment: applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions.
    J Mol Biol, Vol. 303, No. 3. (27 October 2000), pp. 433-446.
    by SM Larson, AA Di Nardo, AR Davidson
    posted to protein-structure residue-covariation by analogAI on 2005-12-21 03:50:29 as ***** along with 6 people and 2 groups ana gbart Haggan cjeans tale bethbromley structural_bioinformatics Bioinformatics
  • 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 protein-structure residue-covariation by analogAI on 2005-12-21 03:34:47 as ***** along with 15 people and 5 groups stevanspringer Einat marcius eckart_bindewald dgront caporaso sriram_s choonpeng Haggan rabio mottonen zambujo mingzhi bethbromley ca3295 structural_bioinformatics FAB-lab biomedical-nlp BioinfoCIPF SGU-CIPF
  • FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties.
    J Mol Biol, Vol. 310, No. 1. (29 June 2001), pp. 243-257.
    by J Shi, TL Blundell, K Mizuguchi
    posted to protein-structure sequencealignment structuralalignment by analogAI on 2005-12-03 00:21:11 as ** along with 6 people and 1 group miguel bicko massivemayhem medic0747 sebk TOchi OPIG
  • notes Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels.
    Proteins, Vol. 14, No. 2. (October 1992), pp. 309-323.
    by RB Russell, GJ Barton
    posted to protein-structure structuralalignment by analogAI on 2005-12-01 01:07:46 as ***** along with 2 people chad_davis jefferlyemerson
  • Multiple structural alignment by secondary structures: algorithm and applications.
    Protein Sci, Vol. 12, No. 11. (November 2003), pp. 2492-2507.
    by O Dror, H Benyamini, R Nussinov, HJ Wolfson
    posted to protein-structure structuralalignment by analogAI on 2005-12-01 00:02:06 as ** along with 2 people ziquje dimka
  • Determining the roles of different chain fragments in recognition of immunoglobulin fold
    Protein Eng., Vol. 15, No. 1. (1 January 2002), pp. 13-19.
    by B Reva, A Kister, S Topiol, I Gelfand
    posted to immunoglobulin protein-structure proteinfolding by analogAI on 2005-11-29 05:47:58 as **
  • notes The importance of loop length in the folding of an immunoglobulin domain
    Protein Engineering, Design and Selection, Vol. 17, No. 5. (1 May 2004), pp. 443-453.
    by Caroline F Wright, John Christodoulou, Christopher M Dobson, Jane Clarke
    posted to immunoglobulin protein-structure proteinfolding by analogAI on 2005-11-29 05:46:21 as *
  • notes A method for simultaneous alignment of multiple protein structures.
    Proteins, Vol. 56, No. 1. (1 July 2004), pp. 143-156.
    by M Shatsky, R Nussinov, HJ Wolfson
    posted to protein-structure structuralalignment by analogAI on 2005-11-28 05:22:26 as ***** along with 3 people nachtalp j3xucite carlescorbi
  • Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming.
    J Mol Biol, Vol. 212, No. 2. (20 March 1990), pp. 403-428.
    by A Sali, TL Blundell
    posted to protein-structure sequencealignment structuralalignment by analogAI on 2005-11-24 01:00:06 as ***
  • An integrated approach to the analysis and modeling of protein sequences and structures. III. A comparative study of sequence conservation in protein structural families using multiple structural alignments.
    J Mol Biol, Vol. 301, No. 3. (18 August 2000), pp. 691-711.
    by AS Yang, B Honig
    posted to protein-structure sequencealignment structuralalignment by analogAI on 2005-11-23 23:47:02 as *****
  • An integrated approach to the analysis and modeling of protein sequences and structures. II. On the relationship between sequence and structural similarity for proteins that are not obviously related in sequence.
    J Mol Biol, Vol. 301, No. 3. (18 August 2000), pp. 679-689.
    by AS Yang, B Honig
    posted to protein-structure structuralalignment by analogAI on 2005-11-23 23:46:13 as **** along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
  • An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structural alignment and a quantitative measure for protein structural distance.
    J Mol Biol, Vol. 301, No. 3. (18 August 2000), pp. 665-678.
    by AS Yang, B Honig
    posted to protein-structure structuralalignment by analogAI on 2005-11-23 23:40:39 as **** along with 2 people and 2 groups ana dimka structural_bioinformatics Bioinformatics
  • An attempt to define allergen-specific molecular surface features: a bioinformatic approach
    Bioinformatics, Vol. 21, No. 23. (1 December 2005), pp. 4201-4204.
    by Ruta Furmonaviciene, Brian J Sutton, Fabian Glaser, Charlie A Laughton, Nick Jones, Herb F Sewell, Farouk Shakib
    posted to allergy protein-structure proteinrecognition by analogAI on 2005-11-23 08:25:09 as **
  • Frequency of gaps observed in a structurally aligned protein pair database suggests a simple gap penalty function
    Nucl. Acids Res., Vol. 32, No. 9. (20 May 2004), pp. 2838-2843.
    by Nalin C Goonesekere, Byungkook Lee
    posted to protein-structure structuralalignment by analogAI on 2005-11-22 02:43:01 as **** along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
  • notes Protein structure alignment by incremental combinatorial extension (CE) of the optimal path.
    Protein Eng, Vol. 11, No. 9. (September 1998), pp. 739-747.
    by IN Shindyalov, PE Bourne
    posted to protein-structure structuralalignment by analogAI on 2005-11-22 02:42:03 as ***** along with 7 people and 2 groups sim82 nigham jwm dgront rabio siebertm Inchoate Radiation_Damage Stressosome
  • MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison
    Protein Sci, Vol. 11, No. 11. (1 November 2002), pp. 2606-2621.
    by Angel R Ortiz, Charlie E Strauss, Osvaldo Olmea
    posted to protein-structure structuralalignment by analogAI on 2005-11-19 02:09:13 as **** along with 5 people and 2 groups sebk ana iakes dimka jwm structural_bioinformatics Bioinformatics
  • Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins
    Bioinformatics, Vol. 21, No. 7. (01 April 2005), pp. 1010-1019.
    by Yuan Xin, Bystroff Christopher
    posted to protein-structure structuralalignment by analogAI on 2005-11-19 02:07:51 as ****
  • Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures.
    J Mol Biol, Vol. 346, No. 4. (4 March 2005), pp. 1173-1188.
    by R Kolodny, P Koehl, M Levitt
    posted to protein-structure review-article structuralalignment by analogAI on 2005-11-19 01:53:49 as read along with 5 people and 2 groups reyez karbak ana lulab balajis structural_bioinformatics Bioinformatics
  • Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
    Acta Crystallographica Section D: Biological Crystallography, Vol. 60, No. 1. (01 December 2004), pp. 2256-2268.
    by Krissinel, , Henrick,
    posted to protein-structure structuralalignment by analogAI on 2005-11-19 01:51:43 as ***** along with 3 people and 4 groups barry jwm robert structural_bioinformatics Radiation_Damage Stressosome Bioinformatics
  • LGA: A method for finding 3D similarities in protein structures.
    Nucleic Acids Res, Vol. 31, No. 13. (1 July 2003), pp. 3370-3374.
    by A Zemla
    posted to protein-structure structuralalignment by analogAI on 2005-11-19 01:42:19 as ***** along with 3 people and 2 groups karbak ana vavi structural_bioinformatics Bioinformatics
  • Protein structure alignment using environmental profiles
    Protein Eng., Vol. 13, No. 8. (1 August 2000), pp. 535-543.
    by Jongsun Jung, Byungkook Lee
    posted to protein-structure structuralalignment by analogAI on 2005-11-19 01:33:31 as *****
  • Structural Bioinformatics (Methods of Biochemical Analysis)
    (24 February 2003)
    by Philip E Bourne, Helge Weissig
    posted to protein-structure review-article by analogAI on 2005-11-19 01:30:45 as ****
  • Protein structure comparison using the markov transition model of evolution.
    Proteins, Vol. 41, No. 1. (1 October 2000), pp. 108-122.
    by T Kawabata, K Nishikawa
    posted to protein-structure structuralalignment by analogAI on 2005-11-19 01:28:02 as ***** along with 1 person nigham
  • Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point.
    Protein Sci, Vol. 13, No. 7. (July 2004), pp. 1865-1874.
    by VA Ilyin, A Abyzov, CM Leslin
    posted to protein-structure structuralalignment by analogAI on 2005-11-19 01:19:04 as ***** along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
  • notes Multiple flexible structure alignment using partial order graphs
    Bioinformatics, Vol. 21, No. 10. (15 May 2005), pp. 2362-2369.
    by Yuzhen Ye, Adam Godzik
    posted to protein-structure structuralalignment by analogAI on 2005-11-19 01:15:26 as *****
  • 3DCoffee: combining protein sequences and structures within multiple sequence alignments.
    J Mol Biol, Vol. 340, No. 2. (2 July 2004), pp. 385-395.
    by O O'Sullivan, K Suhre, C Abergel, DG Higgins, C Notredame
    posted to protein-structure sequencealignment structuralalignment by analogAI on 2005-11-16 19:09:35 as * along with 4 people and 4 groups nickolay edvin ana jwm structural_bioinformatics Radiation_Damage Stressosome Bioinformatics
  • A novel database of disulfide patterns and its application to the discovery of distantly related homologs.
    J Mol Biol, Vol. 335, No. 4. (23 January 2004), pp. 1083-1092.
    by HW van Vlijmen, A Gupta, LS Narasimhan, J Singh
    posted to disulfides protein-structure by analogAI on 2005-11-16 19:07:12 as read
  • A classification of disulfide patterns and its relationship to protein structure and function.
    Protein Sci, Vol. 13, No. 8. (August 2004), pp. 2045-2058.
    by A Gupta, HW Van Vlijmen, J Singh
    posted to disulfides protein-structure by analogAI on 2005-11-16 19:03:51 as *
  • 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 protein-structure proteinfolding by analogAI on 2005-11-16 19:01:01 as read along with 14 people and 5 groups ana barry lna bpb Einat balajis marcius gbart nirfriedman caporaso massivemayhem mingzhi bethbromley ca3295 structural_bioinformatics Bioinformatics biomedical-nlp BioinfoCIPF SGU-CIPF
  • Evolutionarily conserved pathways of energetic connectivity in protein families.
    Science, Vol. 286, No. 5438. (8 October 1999), pp. 295-299.
    by SW Lockless, R Ranganathan
    posted to protein-structure residue-covariation by analogAI on 2005-11-16 18:46:35 as ***** along with 2 people lna gbart
  • A single backmutation in the human kIV framework of a previously unsuccessfully humanized antibody restores the binding activity and increases the secretion in cos cells.
    Mol Immunol, Vol. 36, No. 11-12. (August 1999), pp. 709-719.
    by JW Saldanha, AC Martin, OJ Léger
    posted to cdr immunoglobulin protein-structure by analogAI on 2005-11-16 18:34:18 as **
  • A new progressive-iterative algorithm for multiple structure alignment
    Bioinformatics, Vol. 21, No. 15. (1 August 2005), pp. 3255-3263.
    by Dmitry Lupyan, Alejandra Leo-Macias, Angel R Ortiz
    posted to protein-structure structuralalignment by analogAI on 2005-11-12 01:27:23 as *** along with 3 people and 2 groups ana dimka insectopalo structural_bioinformatics Bioinformatics
  • notes MultiProt - A Multiple Protein Structural Alignment Algorithm
    Vol. 2452 (2002), pp. 235-250.
    by Maxim Shatsky, Ruth Nussinov, Haim J Wolfson
    posted to protein-structure structuralalignment by analogAI on 2005-11-12 00:00:45 as ****
  • How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins.
    J Mol Biol, Vol. 136, No. 3. (25 January 1980), pp. 225-270.
    by AM Lesk, C Chothia
    posted to protein-structure by analogAI on 2005-11-11 22:22:29 as **** along with 1 person and 1 group Einat structural_bioinformatics
  • Protein--protein recognition: juxtaposition of domain and interface cores in immunoglobulins and other sandwich-like proteins.
    J Mol Biol, Vol. 342, No. 2. (10 September 2004), pp. 665-679.
    by V Potapov, V Sobolev, M Edelman, A Kister, I Gelfand
    posted to immunoglobulin protein-structure proteinrecognition by analogAI on 2005-11-11 22:05:23 as **
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