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analogAIs library [68 articles]

Neue Artikel in analogAIs Bibliothek.
  • 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 **
  • 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
  • Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: an information theoretic analysis.
    Proc Natl Acad Sci U S A, Vol. 90, No. 15. (1 August 1993), pp. 7176-7180.
    by BT Korber, RM Farber, DH Wolpert, AS Lapedes
    posted to informationtheory residue-covariation by analogAI on 2006-08-04 02:34:46 as read
  • Covariability of V3 loop amino acids.
    AIDS Res Hum Retroviruses, Vol. 12, No. 15. (10 October 1996), pp. 1401-1411.
    by PJ Bickel, PC Cosman, RA Olshen, PC Spector, AG Rodrigo, JI Mullins
    posted to informationtheory residue-covariation by analogAI on 2006-08-04 02:34:07 as read
  • 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
  • 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
  • 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 **
  • 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
  • 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
  • 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 14 people and 3 groups 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
  • 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 **
  • Position-based sequence weights.
    J Mol Biol, Vol. 243, No. 4. (4 November 1994), pp. 574-578.
    by S Henikoff, JG Henikoff
    posted to sequencealignment by analogAI on 2005-12-15 00:16:53 as read along with 1 person and 1 group Einat structural_bioinformatics
  • 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
  • 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 **
  • 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
  • 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 ***
  • Sequence logos: a new way to display consensus sequences.
    Nucleic Acids Res, Vol. 18, No. 20. (25 October 1990), pp. 6097-6100.
    by TD Schneider, RM Stephens
    posted to sequencelogos by analogAI on 2005-11-24 10:27:39 as read along with 2 people and 1 group indigoviolet yevishere EisenLab
  • WebLogo: A Sequence Logo Generator
    Genome Res., Vol. 14, No. 6. (1 June 2004), pp. 1188-1190.
    by Gavin E Crooks, Gary Hon, John-Marc Chandonia, Steven E Brenner
    posted to sequencelogos by analogAI on 2005-11-24 10:25:50 as read along with 4 people and 2 groups indigoviolet xiaobeizhao sobolevnrm yevishere EisenLab baker-group
  • 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 **
  • The biology of IGE and the basis of allergic disease.
    Annu Rev Immunol, Vol. 21 (2003), pp. 579-628.
    by HJ Gould, BJ Sutton, AJ Beavil, RL Beavil, N McCloskey, HA Coker, D Fear, L Smurthwaite
    posted to allergy ige immunoglobulin review-article by analogAI on 2005-11-23 07:59:51 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 6 people and 2 groups 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 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 ****
  • notes Fast small molecule similarity searching with multiple alignment profiles of molecules represented in one-dimension.
    J Med Chem, Vol. 48, No. 22. (3 November 2005), pp. 6980-6990.
    by N Wang, RK DeLisle, DJ Diller
    posted to smallmolecule by analogAI on 2005-11-19 02:05:00 as read
  • 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 4 people and 2 groups 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
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