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di siebertm library [68 articles]

Articoli aggiunti di recente nella biblioteca di siebertm .
  • Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.
    Biopolymers, Vol. 22, No. 12. (December 1983), pp. 2577-2637.
    by W Kabsch, C Sander
    posted to assignment dssp secondary structure by siebertm on 2007-05-26 11:32:17 as *
  • Network analysis of protein structures identifies functional residues
    Journal of Molecular Biology, Vol. 344, No. 4. (3 December 2004), pp. 1135-1146.
    by G Amitai, A Shemesh, E Sitbon, M Shklar, D Netanely, Venger, S Pietrokovski
    posted to analysis closeness functional network of protein residues structures by siebertm on 2007-05-22 16:06:36 as read along with 7 people and 1 group chrn vavi bicko Einat amitai sriram_s massivemayhem structural_bioinformatics
  • Mining protein family specific residue packing patterns from protein structure graphs
    (2004), pp. 308-315.
    by J Huan, W Wang, D Bandyopadhyay, J Snoeyink, J Prins, A Tropsha
    posted to family function mining patterns prediction protein residue specific structure subgraph tessellation voronoi by siebertm on 2007-05-22 16:04:59 as read
  • Protein function prediction using local 3D templates.
    J Mol Biol (11 July 2005)
    by RA Laskowski, JD Watson, JM Thornton
    posted to 3d function local prediction protein reverse templates by siebertm on 2007-05-22 16:01:24 as read along with 7 people mdimmic shadowman chrn gbart MaggieYe yoonk jwm
  • ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information.
    Bioinformatics, Vol. 19, No. 1. (January 2003), pp. 163-164.
    by F Glaser, T Pupko, I Paz, RE Bell, D Bechor-Shental, E Martz, N Ben-Tal
    posted to consurf detection functional information mapping phylogenetic proteins regions surface by siebertm on 2007-05-22 14:41:58 as * along with 2 people chrn bicko
  • Structural clusters of evolutionary trace residues are statistically significant and common in proteins.
    J Mol Biol, Vol. 316, No. 1. (8 February 2002), pp. 139-154.
    by S Madabushi, H Yao, M Marsh, DM Kristensen, A Philippi, ME Sowa, O Lichtarge
    posted to clusters evolutionary proteins significance statistical structural trace by siebertm on 2007-05-22 14:40:35 as * along with 1 person sriram_s
  • Evolutionary predictions of binding surfaces and interactions.
    Curr Opin Struct Biol, Vol. 12, No. 1. (February 2002), pp. 21-27.
    by O Lichtarge, ME Sowa
    posted to binding conservation evolution interactions prediction protein surfaces by siebertm on 2007-05-22 14:39:15 as * along with 1 person nickolay
  • Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases.
    J Mol Biol, Vol. 281, No. 5. (4 September 1998), pp. 949-968.
    by JS Fetrow, J Skolnick
    posted to fff forms function functional fuzzy local patterns prediction protein structural by siebertm on 2007-05-22 14:20:44 as read along with 1 person sriram_s
  • 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 alignment ce comparison protein structure by siebertm on 2007-05-22 13:53:06 as * along with 10 people and 2 groups sebk reyez pjcite nigham jwm analogAI dgront rabio Inchoate sim82 Radiation_Damage Stressosome
  • Protein structure comparison by alignment of distance matrices.
    J Mol Biol, Vol. 233, No. 1. (5 September 1993), pp. 123-138.
    by L Holm, C Sander
    posted to alignment comparison dali distance matrices protein structure by siebertm on 2007-05-22 13:51:42 as * along with 6 people and 2 groups tjimenez BragilMassoud ana nigham dgront sim82 structural_bioinformatics Bioinformatics
  • PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways.
    Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)
    by H Mi, N Guo, A Kejariwal, PD Thomas
    posted to database hmm interpro panther protein sequences by siebertm on 2007-05-22 12:24:27 as * along with 4 people bootsy skumagai thomaskelder guhjy
  • Gene3D: modelling protein structure, function and evolution.
    Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006)
    by C Yeats, M Maibaum, R Marsden, M Dibley, D Lee, S Addou, CA Orengo
    posted to database families gene3d interpro protein by siebertm on 2007-05-22 12:22:24 as * along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
  • The SUPERFAMILY database in 2007: families and functions.
    Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)
    by D Wilson, M Madera, C Vogel, C Chothia, J Gough
    posted to database families hmm interpro protein superfamily by siebertm on 2007-05-22 12:20:02 as * along with 1 person and 1 group Einat structural_bioinformatics
  • PIRSF: family classification system at the Protein Information Resource.
    Nucleic Acids Res, Vol. 32, No. Database issue. (1 January 2004)
    by CH Wu, A Nikolskaya, H Huang, LS Yeh, DA Natale, CR Vinayaka, ZZ Hu, R Mazumder, S Kumar, P Kourtesis, RS Ledley, BE Suzek, L Arminski, Y Chen, J Zhang, JL Cardenas, S Chung, J Castro-Alvear, G Dinkov, WC Barker
    posted to classification database family interpro pirsf by siebertm on 2007-05-22 12:18:30 as * along with 1 person Cortel
  • The TIGRFAMs database of protein families.
    Nucleic Acids Res, Vol. 31, No. 1. (1 January 2003), pp. 371-373.
    by DH Haft, JD Selengut, O White
    posted to database families hmm interpro protein tigrfam by siebertm on 2007-05-22 12:16:47 as * along with 2 people Cortel wenhan
  • SMART 5: domains in the context of genomes and networks.
    Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006)
    by I Letunic, RR Copley, B Pils, S Pinkert, J Schultz, P Bork
    posted to database domains hmm interpro protein smart by siebertm on 2007-05-22 12:15:21 as * along with 1 person chad_davis
  • Pfam: clans, web tools and services.
    Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006)
    by RD Finn, J Mistry, B Schuster-Böckler, S Griffiths-Jones, V Hollich, T Lassmann, S Moxon, M Marshall, A Khanna, R Durbin, SR Eddy, EL Sonnhammer, A Bateman
    posted to database families hmm interpro pfam protein by siebertm on 2007-05-22 12:13:43 as * along with 11 people cerca gbart dullhunk massivemayhem cjeans lpfernandes pablomendes antonkratz natstreet Lombardo_7 phoenixzxl
  • The ProDom database of protein domain families: more emphasis on 3D.
    Nucleic Acids Res, Vol. 33, No. Database issue. (1 January 2005)
    by C Bru, E Courcelle, S Carrère, Y Beausse, S Dalmar, D Kahn
    posted to clustering database interpro prodom sequence by siebertm on 2007-05-22 12:11:51 as * along with 2 people cjeans gulkur
  • PRINTS and its automatic supplement, prePRINTS.
    Nucleic Acids Res, Vol. 31, No. 1. (1 January 2003), pp. 400-402.
    by TK Attwood, P Bradley, DR Flower, A Gaulton, N Maudling, AL Mitchell, G Moulton, A Nordle, K Paine, P Taylor, A Uddin, C Zygouri
    posted to database fingerprints interpro prints pssm by siebertm on 2007-05-22 12:04:33 as * along with 1 person Cortel
  • Basic local alignment search tool.
    J Mol Biol, Vol. 215, No. 3. (5 October 1990), pp. 403-410.
    by SF Altschul, W Gish, W Miller, EW Myers, DJ Lipman
    posted to alignment blast heuristic local sequence by siebertm on 2007-05-22 11:46:33 as * along with 46 people and 6 groups treangen pwais mmartin tharris dmp camster davidng evaf dragonrez jwm jmeppley Ayest RMGraze ea yas balajis alexg indigoviolet moborg arcticrasta dullhunk dgront caporaso michC myui BioNica CitoJam rabio timflutre lusk cjeans incovoma beatrizfernandez wenhan jtomasch GustavoLacerda sgoetz ichbins81 jofiel Thaverkamp shung marti hervelequere ashaytan benwei granujilla C. elegans / WormBase dbk-lab EisenLab T_lab biomedical-nlp Microbial-Ecology
  • ProFunc: a server for predicting protein function from 3D structure.
    Nucleic Acids Res, Vol. 33, No. Web Server issue. (1 July 2005)
    by RA Laskowski, JD Watson, JM Thornton
    posted to function prediction profunc protein sequence server structure by siebertm on 2007-05-20 16:07:14 as read along with 1 person gbart
  • Evolution of protein function, from a structural perspective.
    Curr Opin Chem Biol, Vol. 3, No. 5. (October 1999), pp. 548-556.
    by AE Todd, CA Orengo, JM Thornton
    posted to evolution function protein structure by siebertm on 2007-05-20 14:19:19 as * along with 2 people renatomilani ucbcjbm
  • The relationship between protein structure and function: a comprehensive survey with application to the yeast genome
    Journal of Molecular Biology, Vol. 288, No. 1. (23 April 1999), pp. 147-164.
    by H Hegyi, M Gerstein
    posted to function protein relationship structure yeast by siebertm on 2007-05-20 14:16:31 as * along with 3 people and 1 group Einat eweaver tny structural_bioinformatics
  • Protein folds and functions.
    Structure, Vol. 6, No. 7. (15 July 1998), pp. 875-884.
    by AC Martin, CA Orengo, EG Hutchinson, S Jones, M Karmirantzou, RA Laskowski, JB Mitchell, C Taroni, JM Thornton
    posted to fold function protein relationship by siebertm on 2007-05-20 14:14:10 as *
  • Structure-based assignment of the biochemical function of a hypothetical protein: a test case of structural genomics.
    Proc Natl Acad Sci U S A, Vol. 95, No. 26. (22 December 1998), pp. 15189-15193.
    by TI Zarembinski, LW Hung, HJ Mueller-Dieckmann, KK Kim, H Yokota, R Kim, SH Kim
    posted to assignment complexes function genomics protein-ligand structural by siebertm on 2007-05-20 12:52:43 as * along with 1 person and 1 group Sarat MAGGIE
  • Protein superfamilies and domain superfolds.
    Nature, Vol. 372, No. 6507. (15 December 1994), pp. 631-634.
    by CA Orengo, DT Jones, JM Thornton
    posted to comparison domain protein structure superfamilies superfolds by siebertm on 2007-05-18 22:27:58 as * along with 1 person Evangelia
  • Identification of homology in protein structure classification
    Nat Struct Mol Biol, Vol. 8, No. 11. (November 2001), pp. 953-957.
    by S Dietmann, L Holm
    posted to classification comparison homology protein structure by siebertm on 2007-05-18 22:26:42 as *
  • New developments in the InterPro database.
    Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)
    by NJ Mulder, R Apweiler, TK Attwood, A Bairoch, A Bateman, D Binns, P Bork, V Buillard, L Cerutti, R Copley, E Courcelle, U Das, L Daugherty, M Dibley, R Finn, W Fleischmann, J Gough, D Haft, N Hulo, S Hunter, D Kahn, A Kanapin, A Kejariwal, A Labarga, PS Langendijk-Genevaux, D Lonsdale, R Lopez, I Letunic, M Madera, J Maslen, C Mcanulla, J Mcdowall, J Mistry, A Mitchell, AN Nikolskaya, S Orchard, C Orengo, R Petryszak, JD Selengut, CJ Sigrist, PD Thomas, F Valentin, D Wilson, CH Wu, C Yeats
    posted to database gene3d integrated interpro panther pfam pirsf prints prodom prosite resource smart superfamily tigrfams by siebertm on 2007-05-18 21:26:35 as read along with 4 people guhjy balajis sgoetz pablomendes
  • The ASTRAL compendium in 2004.
    Nucleic Acids Res, Vol. 32, No. Database issue. (1 January 2004)
    by JM Chandonia, G Hon, NS Walker, L Lo Conte, P Koehl, M Levitt, SE Brenner
    posted to astral database domains protein scop sequences by siebertm on 2007-05-18 20:35:03 as ** along with 6 people chad_davis sriram_s aengisch rabio saunders reyez
  • The ASTRAL compendium for protein structure and sequence analysis.
    Nucleic Acids Res, Vol. 28, No. 1. (1 January 2000), pp. 254-256.
    by SE Brenner, P Koehl, M Levitt
    posted to astral database domains protein scop sequences by siebertm on 2007-05-18 20:34:08 as ** along with 3 people rabio cjeans gulkur
  • Conformational Changes Observed in Enzyme Crystal Structures upon Substrate Binding
    Journal of Molecular Biology, Vol. 346, No. 1. (11 February 2005), pp. 21-28.
    by A Gutteridge, J Thornton
    posted to catalysis changes conformational enzyme by siebertm on 2007-05-16 16:23:37 as *
  • Conformational change in substrate binding, catalysis and product release: an open and shut case?
    FEBS Lett, Vol. 567, No. 1. (1 June 2004), pp. 67-73.
    by A Gutteridge, J Thornton
    posted to catalysis changes conformational enzyme by siebertm on 2007-05-16 16:22:05 as * along with 2 people alexg gbart
  • Multiple conformational changes in enzyme catalysis.
    Biochemistry, Vol. 41, No. 26. (2 July 2002), pp. 8221-8228.
    by GG Hammes
    posted to catalysis changes conformational entropy enzyme by siebertm on 2007-05-16 16:20:31 as * along with 2 people lna nigham
  • On the Magnitude and Specificity of Medium Effects in Enzyme-like Catalysts for Proton Transfer
    J. Org. Chem., Vol. 66, No. 17. (24 August 2001), pp. 5866-5874.
    by F Hollfelder, AJ Kirby, DS Tawfik
    posted to catalytic effects environment enzyme medium non-polar residues by siebertm on 2007-05-16 12:32:51 as *
  • Metallo-enzyme catalysis.
    Chem Commun (Camb), No. 10. (21 May 2003), pp. 1109-1113.
    by RJ Williams
    posted to catalysis ions metal metallo-enzyme by siebertm on 2007-05-15 13:53:51 as **
  • The extended environment of mononuclear metal centers in protein structures.
    Proc Natl Acad Sci U S A, Vol. 94, No. 26. (23 December 1997), pp. 14225-14230.
    by S Karlin, ZY Zhu, KD Karlin
    posted to binding environment metal protein sites structures by siebertm on 2007-05-15 13:32:58 as **
  • Understanding nature's catalytic toolkit.
    Trends Biochem Sci (5 October 2005)
    by A Gutteridge, JM Thornton
    posted to active catalytic enzyme residues sites toolkit units by siebertm on 2007-05-15 13:31:22 as ** along with 10 people and 4 groups ana jwm Einat alexg gbart eweaver tny noby grottenolm sim82 structural_bioinformatics Radiation_Damage Stressosome Bioinformatics
  • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
    Nucleic Acids Res, Vol. 25, No. 17. (1 September 1997), pp. 3389-3402.
    by SF Altschul, TL Madden, AA Schäffer, J Zhang, Z Zhang, W Miller, DJ Lipman
    posted to blast gapped psi-blast by siebertm on 2007-05-14 13:07:17 as * along with 51 people and 4 groups daforerog nlapalu sebk tjimenez shung pwais dakelley knaseanka setar iakes miguel kaarsinogen bjorns bicko jmeppley chad_davis balajis nuke2005 eweaver david_parsons indigoviolet dullhunk robert dgront happy_manatee caporaso treangen kengg manzanita leelarcombe CitoJam jdelcampo aengisch rabio massivemayhem mirzazadeh azazello sujaikumar beatrizfernandez GustavoLacerda adijr viktor21614 mijam grottenolm bandrewfox edvin newton1234 mariakmejia granujilla marti CharlesM EisenLab biomedical-nlp Microbial-Ecology Plantandetc
  • Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes.
    Proc Natl Acad Sci U S A, Vol. 87, No. 6. (March 1990), pp. 2264-2268.
    by S Karlin, SF Altschul
    posted to features general schemes scoring sequence significance statistical by siebertm on 2007-05-14 13:06:16 as * along with 7 people and 1 group kaspermunch AaronDarling rabio timflutre cjeans adijr karfunkel Bioinformatics
  • Local alignment statistics.
    Methods Enzymol, Vol. 266 (1996), pp. 460-480.
    by SF Altschul, W Gish
    posted to alignment local statistics by siebertm on 2007-05-14 13:04:37 as *
  • A model for statistical significance of local similarities in structure.
    J Mol Biol, Vol. 326, No. 5. (7 March 2003), pp. 1307-1316.
    by A Stark, S Sunyaev, RB Russell
    posted to local measure significance statistical structure template by siebertm on 2007-05-14 12:46:22 as ** along with 8 people and 2 groups karbak ana nigham chad_davis thamelry nickolay robert scis0000001 structural_bioinformatics Bioinformatics
  • Analysis of catalytic residues in enzyme active sites.
    J Mol Biol, Vol. 324, No. 1. (15 November 2002), pp. 105-121.
    by GJ Bartlett, CT Porter, N Borkakoti, JM Thornton
    posted to active analysis catalytic enzyme residues sites by siebertm on 2007-05-14 10:55:17 as ** along with 4 people baaden gbart nickolay sriram_s
  • An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis.
    Bioinformatics, Vol. 19, No. 13. (1 September 2003), pp. 1644-1649.
    by JA Barker, JM Thornton
    posted to 3d algorithm jess search template by siebertm on 2007-05-12 15:11:38 as ** along with 6 people and 2 groups shadowman tjimenez jwm gbart tny chgjb Radiation_Damage Stressosome
  • The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data.
    Nucleic Acids Res, Vol. 32, No. Database issue. (1 January 2004)
    by CT Porter, GJ Bartlett, JM Thornton
    posted to active catalytic database enzyme residues sites by siebertm on 2007-05-12 15:10:02 as read along with 9 people and 2 groups tjimenez baaden chrn jwm gbart tny sriram_s massivemayhem grottenolm Radiation_Damage Stressosome
  • ScanProsite: a reference implementation of a PROSITE scanning tool.
    Appl Bioinformatics, Vol. 1, No. 2. (2002), pp. 107-108.
    by A Gattiker, E Gasteiger, A Bairoch
    posted to prosite scanning tool by siebertm on 2007-05-12 15:08:37 as **
  • PROSITE: a documented database using patterns and profiles as motif descriptors
    Brief Bioinform, Vol. 3, No. 3. (1 January 2002), pp. 265-274.
    by CJA Sigrist, L Cerutti, N Hulo, A Gattiker, L Falquet, M Pagni, A Bairoch, P Bucher
    posted to database patterns profiles prosite sequence by siebertm on 2007-05-12 15:03:43 as read along with 2 people shung jteyra
  • The PROSITE database.
    Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006)
    by N Hulo, A Bairoch, V Bulliard, L Cerutti, E De Castro, PS Langendijk-Genevaux, M Pagni, CJ Sigrist
    posted to database patterns profiles prosite sequence by siebertm on 2007-05-12 15:01:05 as read along with 5 people and 1 group yas happy_manatee sriram_s neils massivemayhem T_lab
  • The classification of amino acid conservation.
    J Theor Biol, Vol. 119, No. 2. (21 March 1986), pp. 205-218.
    by WR Taylor
    posted to acid amino classification conservation by siebertm on 2007-05-05 15:27:19 as ** along with 1 person gisle
  • T-Coffee: a novel method for fast and accurate multiple sequence alignment.
    J Mol Biol, Vol. 302, No. 1. (8 September 2000), pp. 205-217.
    by C Notredame, DG Higgins, J Heringa
    posted to alignment check consistency multiple sequence by siebertm on 2007-05-04 13:45:32 as read along with 10 people and 1 group sebk miguel dayjm indigoviolet ffranca treangen Haggan adijr marti newton1234 EisenLab
  • The Hungarian method for the assignment problem
    Naval Research Logistic Quarterly, Vol. 2 (1955), pp. 83-97.
    by HW Kuhn
    posted to algorithm bipartite graphs hungarian matching by siebertm on 2007-05-03 20:23:05 as * along with 1 person maelp
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