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marti's library [84 articles]

最近录入 marti's 文献库.
  • A mathematical theory of communication
    SIGMOBILE Mob. Comput. Commun. Rev., Vol. 5, No. 1. (January 2001), pp. 3-55.
    by CE Shannon
    posted to entropy by marti on 2008-08-27 16:07:58 as * along with 15 people and 1 group ssn ansobol chrn kristgy luispedro scottr davidmihalcik bigbossman lop michaelmampaey alexzeh dcoates almansa champak gfacciol ADMiRes
  • 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 dssp secondary-structure by marti on 2008-08-26 17:38:55 as * along with 15 people kaarsinogen lna chad_davis wouterboomsma penka ffranca dgront choonpeng leelarcombe rabio gisle medic0747 martainn chgjb mschofie
  • Inferring protein DNA dependencies using motif alignments and mutual information
    Bioinformatics, Vol. 23, No. 13. (1 July 2007), pp. i297-304.
    by Shaun Mahony, Philip E Auron, Panayiotis V Benos
    posted to mutual-information transcriptionfactor by marti on 2008-08-26 17:30:10 as read along with 1 person nklee
  • Pfam: a comprehensive database of protein domain families based on seed alignments.
    Proteins, Vol. 28, No. 3. (July 1997), pp. 405-420.
    by EL Sonnhammer, SR Eddy, R Durbin
    posted to database profiles by marti on 2008-08-13 18:04:29 as ** along with 5 people pcahan1 cjeans antonkratz ca3295 gulkur
  • Protein binding site prediction using an empirical scoring function.
    Nucleic Acids Res, Vol. 34, No. 13. (2006), pp. 3698-3707.
    by S Liang, C Zhang, S Liu, Y Zhou
    posted to interfaces prediction by marti on 2008-08-13 18:00:57 as read along with 1 person emidio_capriotti
  • 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 by marti on 2008-08-13 17:53:54 as read along with 45 people and 4 groups 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 siebertm adijr viktor21614 mijam grottenolm bandrewfox edvin newton1234 mariakmejia granujilla CharlesM EisenLab biomedical-nlp Microbial-Ecology Plantandetc
  • Identification of protein oligomerization states by analysis of interface conservation.
    Proc Natl Acad Sci U S A, Vol. 98, No. 6. (13 March 2001), pp. 2990-2994.
    by AH Elcock, JA McCammon
    posted to conservation interfaces oligomerization by marti on 2008-08-13 11:47:34 as **** along with 2 people bicko Evangelia
  • Using transcription factor binding site co-occurrence to predict regulatory regions.
    Genome informatics. International Conference on Genome Informatics, Vol. 18 (2007), pp. 109-118.
    by H Klein, M Vingron
    posted to binding prediction transcriptionfactor by marti on 2008-08-07 15:19:52 as read
  • Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis
    Science, Vol. 320, No. 5883. (20 June 2008), pp. 1632-1635.
    by Ari Loytynoja, Nick Goldman
    posted to msa phylogeny by marti on 2008-08-07 15:16:49 as *** along with 22 people and 3 groups bpcusack chad_davis hpaces dinnes gjuggler djkt ArtemPankin phoenixzxl jago marck imtechnology aprasad zwang bmaust bpb michaelbarton Schmidtc AbnerCYH gulsacan emptyhb jlgreen nuin Khavkin's lab iSEEM Green Lab
  • An evaluation of automated homology modelling methods at low target template sequence similarity
    Bioinformatics, Vol. 23, No. 15. (1 August 2007), pp. 1901-1908.
    by James A Dalton, Richard M Jackson
    posted to homology-modelling msa by marti on 2008-08-07 15:13:47 as *** along with 5 people cdeane chad_davis biehl neils pansapiens
  • Atomic contact vectors in protein-protein recognition.
    Proteins, Vol. 53, No. 3. (15 November 2003), pp. 629-639.
    by J Mintseris, Z Weng
    posted to acv obligate-transient by marti on 2008-07-04 16:19:11 as *** along with 1 person bicko
  • Analysis of ordered and disordered protein complexes reveals structural features discriminating between stable and unstable monomers.
    J Mol Biol, Vol. 341, No. 5. (27 August 2004), pp. 1327-1341.
    by K Gunasekaran, CJ Tsai, R Nussinov
    posted to disordered-regions interactions by marti on 2008-07-04 16:17:45 as ** along with 2 people chad_davis allmensch
  • Structural characterisation and functional significance of transient protein-protein interactions.
    J Mol Biol, Vol. 325, No. 5. (31 January 2003), pp. 991-1018.
    by IM Nooren, JM Thornton
    posted to interactions obligate-transient by marti on 2008-07-04 16:14:16 as ** along with 4 people chad_davis drastic ramensky higueruelo
  • Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different.
    BMC Struct Biol, Vol. 5 (16 August 2005)
    by S De, O Krishnadev, N Srinivasan, N Rekha
    posted to interfaces obligate-transient by marti on 2008-07-03 14:08:38 as read along with 4 people bicko choonpeng medic0747 higueruelo
  • NOXclass: prediction of protein-protein interaction types.
    BMC Bioinformatics, Vol. 7 (2006)
    by H Zhu, FS Domingues, I Sommer, T Lengauer
    posted to interactions obligate-transient prediction by marti on 2008-07-03 14:08:12 as read along with 4 people bicko chad_davis conkymacro jteyra
  • KFC Server: interactive forecasting of protein interaction hot spots.
    Nucleic acids research (6 June 2008)
    by Steven J J Darnell, Laura Legault, Julie C C Mitchell
    posted to hotspot interactions prediction by marti on 2008-06-18 18:47:41 as read along with 1 person higueruelo
  • Born to bind: the BTB protein-protein interaction domain.
    BioEssays : news and reviews in molecular, cellular and developmental biology, Vol. 28, No. 12. (December 2006), pp. 1194-1202.
    by R Perez-Torrado, D Yamada, PA Defossez
    posted to binding interactions transcriptionfactor by marti on 2008-06-17 15:04:38 as read
  • FOXO-binding partners: it takes two to tango.
    Oncogene, Vol. 27, No. 16. (7 April 2008), pp. 2289-2299.
    by KE van der Vos, PJ Coffer
    posted to binding transcriptionfactor by marti on 2008-06-17 15:03:34 as read along with 1 person jyuh
  • The biology of eukaryotic promoter prediction--a review.
    Computers & chemistry, Vol. 23, No. 3-4. (15 June 1999), pp. 191-207.
    by AG Pedersen, P Baldi, Y Chauvin, S Brunak
    posted to prediction review transcriptionfactor by marti on 2008-06-17 15:01:42 as read along with 1 person xiaobeizhao
  • Evaluation of local structure alphabets based on residue burial.
    Proteins, Vol. 55, No. 3. (15 May 2004), pp. 508-518.
    by R Karchin, M Cline, K Karplus
    posted to conservation exposure mutual_information by marti on 2008-06-17 14:50:09 as ***
  • Analysis and prediction of functional sub-types from protein sequence alignments
    Journal of Molecular Biology, Vol. 303, No. 1. (13 October 2000), pp. 61-76.
    by Sridhar S Hannenhalli, Robert B Russell
    posted to alignments hmm msa prediction by marti on 2008-05-07 18:00:32 as *** along with 1 person and 2 groups barry structural_bioinformatics Bioinformatics
  • Scoring residue conservation.
    Proteins, Vol. 48, No. 2. (1 August 2002), pp. 227-241.
    by WS Valdar
    posted to conservation review by marti on 2008-05-01 17:00:28 as read along with 7 people and 2 groups barry pansapiens bicko sriram_s cjeans sobolevnrm chad_davis structural_bioinformatics Bioinformatics
  • Identification of transient hub proteins and the possible structural basis for their multiple interactions
    Protein Sci, Vol. 17, No. 1. (1 January 2008), pp. 72-78.
    by Miho Higurashi, Takashi Ishida, Kengo Kinoshita
    posted to interactions obligate-transient by marti on 2008-04-30 15:32:42 as *** along with 4 people bicko chad_davis balicea allmensch
  • Characterization of interfacial solvent in protein complexes and contribution of <I>wet spots</I> to the interface description
    Proteins: Structure, Function, and Bioinformatics, Vol. 67, No. 4. (2007), pp. 1087-1095.
    by Joan Teyra, MT Pisabarro
    posted to interactions interfaces obligate-transient by marti on 2008-04-29 14:10:54 as read along with 4 people bicko choonpeng jteyra Lombardo_7
  • The molecular architecture of protein-protein binding sites
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Dana Reichmann, Ofer Rahat, Mati Cohen, Hani Neuvirth, Gideon Schreiber
    posted to interfaces by marti on 2008-04-25 17:12:33 as read along with 5 people bicko chad_davis choonpeng hmk higueruelo
  • Exploiting residue-level and profile-level interface propensities for usage in binding sites prediction of proteins
    BMC Bioinformatics, Vol. 8 (05 May 2007), 147.
    by Qiwen Dong, Xiaolong Wang, Lei Lin, Yi Guan
    posted to interfaces prediction by marti on 2008-04-25 17:07:59 as read along with 2 people bicko zwang
  • Incorporating background frequency improves entropy-based residue conservation measures
    BMC Bioinformatics, Vol. 7 (17 August 2006), 385.
    by Kai Wang, Ram Samudrala
    posted to conservation measure by marti on 2008-04-24 13:36:08 as read along with 2 people nklee bicko
  • Improved prediction of protein-protein binding sites using a support vector machines approach
    Bioinformatics, Vol. 21, No. 8. (15 April 2005), pp. 1487-1494.
    by James R Bradford, David R Westhead
    posted to interfaces prediction svm by marti on 2008-04-24 13:31:08 as read along with 8 people bicko sriram_s chaleil ameetsoni cjeans Evangelia phoenixzxl OriginalLurch
  • WHISCY: What information does surface conservation yield? Application to data-driven docking.
    Proteins (31 January 2006)
    by Sjoerd J J de Vries, Aalt D J D van Dijk, Alexandre M J J M Bonvin
    posted to docking interfaces prediction by marti on 2008-04-24 12:10:53 as read along with 2 people bicko gloria
  • ProMateus--an open research approach to protein-binding sites analysis.
    Nucleic acids research, Vol. 35, No. Web Server issue. (July 2007)
    by H Neuvirth, U Heinemann, D Birnbaum, N Tishby, G Schreiber
    posted to interfaces by marti on 2008-04-24 12:07:05 as read
  • Prediction-based fingerprints of protein-protein interactions
    Proteins: Structure, Function, and Bioinformatics, Vol. 66, No. 3. (2007), pp. 630-645.
    by Aleksey Porollo, Jaros&lstrok;aw Meller
    posted to interfaces prediction by marti on 2008-04-24 12:00:49 as read along with 2 people bicko choonpeng
  • The Third CAPRI Assessment Meeting Toronto, Canada, April 20-21, 2007.
    Structure, Vol. 15, No. 7. (July 2007), pp. 755-759.
    by J Janin, S Wodak
    posted to interfaces prediction by marti on 2008-04-11 16:13:39 as *** along with 2 people bicko chad_davis
  • TRANSFAC retrieval program: a network model database of eukaryotic transcription regulating sequences and proteins.
    J Comput Biol, Vol. 1, No. 3. (1994), pp. 191-198.
    by R Knüppel, P Dietze, W Lehnberg, K Frech, E Wingender
    posted to transcriptionfactor by marti on 2008-03-26 12:32:03 as ***
  • The TRANSFAC system on gene expression regulation.
    Nucleic Acids Res, Vol. 29, No. 1. (1 January 2001), pp. 281-283.
    by E Wingender, X Chen, E Fricke, R Geffers, R Hehl, I Liebich, M Krull, V Matys, H Michael, R Ohnhäuser, M Prüss, F Schacherer, S Thiele, S Urbach
    posted to transcriptionfactor by marti on 2008-03-25 18:31:17 as *** along with 1 person Takayuki
  • Binding Site Graphs: A New Graph Theoretical Framework for Prediction of Transcription Factor Binding Sites
    PLoS Computational Biology, Vol. 3, No. 5. (1 May 2007), e90.
    by Timothy E Reddy, Charles Delisi, Boris E Shakhnovich
    posted to interfaces prediction transcriptionfactor by marti on 2008-03-10 16:54:13 as read along with 5 people and 1 group aalibes dpollard medic0747 GustavoLacerda mircea EisenLab
  • TRANSFAC: an integrated system for gene expression regulation.
    Nucleic Acids Res, Vol. 28, No. 1. (1 January 2000), pp. 316-319.
    by E Wingender, X Chen, R Hehl, H Karas, I Liebich, V Matys, T Meinhardt, M Prüss, I Reuter, F Schacherer
    posted to transcriptionfactor by marti on 2008-03-07 12:03:37 as *** along with 1 person gpalidwor
  • Automatic transcription factor classifier based on functional domain composition.
    Biochem Biophys Res Commun, Vol. 347, No. 1. (18 August 2006), pp. 141-144.
    by Z Qian, YD Cai, Y Li
    posted to interfaces transcriptionfactor by marti on 2008-03-07 12:03:18 as ***
  • TRANSFAC: transcriptional regulation, from patterns to profiles.
    Nucleic Acids Res, Vol. 31, No. 1. (1 January 2003), pp. 374-378.
    by V Matys, E Fricke, R Geffers, E Gössling, M Haubrock, R Hehl, K Hornischer, D Karas, AE Kel, OV Kel-Margoulis, DU Kloos, S Land, B Lewicki-Potapov, H Michael, R Münch, I Reuter, S Rotert, H Saxel, M Scheer, S Thiele, E Wingender
    posted to transcriptionfactor by marti on 2008-03-07 12:00:41 as **** along with 6 people and 1 group aalibes setar chad_davis GustavoLacerda Auger kmdaily Dead 60's
  • Structure, function, and evolution of transient and obligate protein-protein interactions.
    Proc Natl Acad Sci U S A (25 July 2005)
    by Julian Mintseris, Zhiping Weng
    posted to structure surface by marti on 2008-02-25 12:35:51 as read along with 9 people and 3 groups barry bjorns wiehe julianm bicko chad_davis cjeans Evangelia higueruelo structural_bioinformatics ZLAB Bioinformatics
  • Predicting protein interaction sites: binding hot-spots in proteinprotein and proteinligand interfaces
    Bioinformatics, Vol. 22, No. 11. (1 June 2006), pp. 1335-1342.
    by Burgoyne, J Nicholas, Jackson, M Richard
    posted to hotspot interfaces prediction by marti on 2008-02-18 11:21:51 as read along with 5 people bicko chad_davis nickolay conkymacro ladab
  • Comparative study of several algorithms for flexible ligand docking.
    J Comput Aided Mol Des, Vol. 17, No. 11. (November 2003), pp. 755-763.
    by BD Bursulaya, M Totrov, R Abagyan, CL Brooks
    posted to docking by marti on 2008-01-31 18:12:06 as ** along with 1 person bicko
  • Optimal docking area: a new method for predicting protein-protein interaction sites.
    Proteins, Vol. 58, No. 1. (1 January 2005), pp. 134-143.
    by J Fernandez-Recio, M Totrov, C Skorodumov, R Abagyan
    posted to docking interactions prediction by marti on 2008-01-31 18:10:34 as ** along with 4 people and 2 groups jwm bicko schlauchi cjeans Radiation_Damage Stressosome
  • A structural perspective on protein-protein interactions.
    Curr Opin Struct Biol, Vol. 14, No. 3. (June 2004), pp. 313-324.
    by RB Russell, F Alber, P Aloy, FP Davis, D Korkin, M Pichaud, M Topf, A Sali
    posted to interactions review by marti on 2008-01-31 18:06:16 as ** along with 13 people and 1 group baaden bicko anita chad_davis dgront sriram_s ruvido cjeans Evangelia Pao-Yang higueruelo jteyra timg structure-bii
  • 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 no-tag by marti on 2008-01-31 18:02:09 as ** along with 6 people karbak aalibes baaden bicko chad_davis higueruelo
  • RESTRICTED MOBILITY OF CONSERVED RESIDUES IN PROTEIN-PROTEIN INTERFACES IN MOLECULAR SIMULATIONS.
    Biophys J (28 January 2008)
    by S Bora B Erdemli, O Nuri N Yogurtcu, Metin Turkay, Ruth Nussinov, Ozlem Keskin
    posted to flexibility by marti on 2008-01-31 16:48:00 as ** along with 4 people bicko chad_davis jlh64 higueruelo
  • Computing Ka and Ks with a consideration of unequal transitional substitutions
    BMC Evolutionary Biology, Vol. 6 (02 June 2006), 44.
    by Zhang Zhang, Jun Li, Jun Yu
    posted to kaks by marti on 2008-01-28 17:08:05 as read
  • KaKs_Calculator: calculating Ka and Ks through model selection and model averaging.
    Genomics Proteomics Bioinformatics, Vol. 4, No. 4. (November 2006), pp. 259-263.
    by Z Zhang, J Li, XQ Zhao, J Wang, GK Wong, J Yu
    posted to kaks by marti on 2008-01-28 17:07:49 as read
  • Synonymous and nonsynonymous rate variation in nuclear genes of mammals.
    J Mol Evol, Vol. 46, No. 4. (April 1998), pp. 409-418.
    by Z Yang, R Nielsen
    posted to kaks by marti on 2008-01-28 17:07:36 as read
  • On itinerant water molecules and detectability of protein-protein interfaces through comparative analysis of homologues.
    J Mol Biol, Vol. 369, No. 2. (1 June 2007), pp. 584-595.
    by I Mihalek, I Res, O Lichtarge
    posted to interfaces prediction by marti on 2008-01-28 17:07:19 as ** along with 1 person jteyra
  • Conservation and relative importance of residues across protein-protein interfaces.
    Proc Natl Acad Sci U S A, Vol. 102, No. 43. (25 October 2005), pp. 15447-15452.
    by M Guharoy, P Chakrabarti
    posted to interfaces by marti on 2008-01-28 17:06:50 as ** along with 2 people bicko drastic
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