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analogAIs library [72 articles]

Neue Artikel in analogAIs library ordered by importance.
  • notes Correlated mutations and residue contacts in proteins.
    Proteins, Vol. 18, No. 4. (April 1994), pp. 309-317.
    by U Göbel, C Sander, R Schneider, A Valencia
    posted to protein-sequence residue-covariation by analogAI on 2006-05-05 04:59:39 as ***** along with 3 people gbart dgront cjeans
  • 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
  • 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
  • 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
  • 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 *****
  • 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 6 people and 2 groups nigham jwm dgront rabio siebertm Inchoate Radiation_Damage Stressosome
  • 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 *****
  • 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 *****
  • 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
  • Inaugural Article: Finding important sites in protein sequences
    PNAS, Vol. 99, No. 23. (12 November 2002), pp. 14764-14771.
    by Peter J Bickel, Katherina J Kechris, Philip C Spector, Gary J Wedemayer, Alexander N Glazer
    posted to informationtheory residue-covariation by analogAI on 2006-08-04 02:38:46 as **** along with 2 people nickolay sriram_s
  • notes Gaps in structurally similar proteins: towards improvement of multiple sequence alignment.
    Proteins, Vol. 54, No. 1. (1 January 2004), pp. 71-87.
    by JO Wrabl, NV Grishin
    posted to protein-sequence sequencealignment structuralalignment by analogAI on 2006-06-29 05:45:12 as **** along with 2 people and 2 groups ana barry structural_bioinformatics Bioinformatics
  • 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
  • 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
  • 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
  • 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 4 people and 2 groups 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 ****
  • 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 ****
  • 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
  • HMM Logos for visualization of protein families.
    BMC Bioinformatics, Vol. 5 (21 January 2004)
    by B Schuster-Böckler, J Schultz, S Rahmann
    posted to sequencelogos by analogAI on 2005-11-24 10:29:13 as ***
  • 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 ***
  • 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
  • Cyanobacterial leader peptides for protein secretion
    FEMS Microbiology Letters, Vol. 218, No. 2. (2003), pp. 351-357.
    by Tatiana V Sergeyenko, Dmitry A Los
    posted to signalprotein pcc6803 lichenase glucanase by analogAI on 2008-06-27 11:11:41 as **
  • Synechocystis PCC6803: a euryhaline cyanobacterium
    FEMS Microbiology Letters, Vol. 18, No. 1-2. (1983), pp. 99-102.
    by DL Richardson, RH Reed, WDP Stewart
    posted to pcc6803 halotolerance growth by analogAI on 2008-06-24 22:28:54 as **
  • Conjugative transfer and autonomous replication of a promiscuous IncQ plasmid in the cyanobacterium Synechocystis PCC 6803
    Molecular and General Genetics MGG, Vol. 221, No. 1. (1 March 1990), pp. 129-133.
    by Sabine Kreps, Fabrice Ferino, Christine Mosrin, Jozef Gerits, Max Mergeay, Pierre Thuriaux
    posted to transformation plasmid pcc6803 by analogAI on 2008-06-09 08:49:40 as **
  • A host-vector system for gene cloning in the cyanobacterium Synechocystis PCC 6803
    Molecular and General Genetics MGG, Vol. 204, No. 1. (1 July 1986), pp. 185-191.
    by F Chauvat, L Vries, A Ende, GA Arkel
    posted to transformation pcc6803 by analogAI on 2008-06-09 07:10:46 as **
  • Engineering BioBrick vectors from BioBrick parts
    Journal of Biological Engineering, Vol. 2, No. 5. (14 April 2008)
    by Reshma P Shetty, Drew Endy, Thomas F Knight
    posted to vector transformation biobrick by analogAI on 2008-05-06 05:32:54 as **
  • notes On the Rate of Diatom Growth
    Journal of the Marine Biological Association of the United Kingdom, Vol. 19, No. 1. (1933), pp. 253-276.
    by HW Harvey
    posted to clostorium_nitzschia diatom by analogAI on 2006-11-26 23:28:34 as **
  • CO2 fixation and ethanol production with microalgal photosynthesis and intracellular anaerobic fermentation
    pp. 137-142.
    by A Hirano
    posted to chlamydomonas_reinhardtii chlorella_vulgaris ethanol green_algae by analogAI on 2006-11-04 07:56:24 as **
  • Specificity grafting of human antibody frameworks selected from a phage display library: generation of a highly stable humanized anti-CD22 single-chain Fv fragment
    Protein Eng., Vol. 16, No. 10. (1 October 2003), pp. 753-759.
    by Jurgen Krauss, Michaela A Arndt, Andrew C Martin, Huaitian Liu, Susanna M Rybak
    posted to protein-engineering protein-stability by analogAI on 2006-08-22 20:37:14 as **
  • Identification of differences in the specificity-determining residues of antibodies that recognize antigens of different size: implications for the rational design of antibody repertoires.
    J Mol Recognit, Vol. 17, No. 2. (r 2004), pp. 132-143.
    by JC Almagro
    posted to immunoglobulin proteinrecognition by analogAI on 2006-08-22 20:30:24 as **
  • 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 **
  • Engineering novel binding proteins from nonimmunoglobulin domains
    Nature Biotechnology, Vol. 23, No. 10. (06 October 2005), pp. 1257-1268.
    by Kaspar H Binz, Patrick Amstutz, Andreas Plückthun
    posted to immunoglobulin protein-engineering proteinrecognition by analogAI on 2006-06-03 06:55:34 as **
  • 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 **
  • Information content of individual genetic sequences.
    J Theor Biol, Vol. 189, No. 4. (21 December 1997), pp. 427-441.
    by TD Schneider
    posted to informationtheory sequencealignment statistics by analogAI on 2005-12-16 03:44:49 as **
  • Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology.
    Comput Appl Biosci, Vol. 12, No. 4. (August 1996), pp. 327-345.
    by K Sjölander, K Karplus, M Brown, R Hughey, A Krogh, IS Mian, D Haussler
    posted to sequencealignment statistics by analogAI on 2005-12-16 03:31:32 as **
  • 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
  • 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
  • notes The immunoglobulin fold family: sequence analysis and 3D structure comparisons.
    Protein Eng, Vol. 12, No. 7. (July 1999), pp. 563-571.
    by DM Halaby, A Poupon, J Mornon
    posted to immunoglobulin proteinfolding proteinrecognition by analogAI on 2005-11-29 05:49:42 as ** along with 1 person and 1 group stevanspringer FAB-lab
  • 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 **
  • 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 **
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