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marti's library [74 articles]

Recent papers added to marti's library.
  • 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 obligate-transient acv 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 interactions disordered-regions by marti on 2008-07-04 16:17:45 as ** along with 2 people allmensch chad_davis
  • 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 obligate-transient interactions by marti on 2008-07-04 16:14:16 as ** along with 4 people higueruelo chad_davis drastic ramensky
  • 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 obligate-transient interfaces by marti on 2008-07-03 14:08:38 as read along with 4 people higueruelo bicko choonpeng medic0747
  • NOXclass: prediction of protein-protein interaction types.
    BMC Bioinformatics, Vol. 7 (2006)
    by H Zhu, FS Domingues, I Sommer, T Lengauer
    posted to prediction obligate-transient interactions by marti on 2008-07-03 14:08:12 as read along with 3 people bicko chad_davis conkymacro
  • 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 prediction interactions hotspot 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 transcriptionfactor interactions binding 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 transcriptionfactor binding 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 transcriptionfactor review prediction by marti on 2008-06-17 15:01:42 as read
  • 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 mutual_information exposure conservation 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 prediction msa hmm alignments 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 review conservation by marti on 2008-05-01 17:00:28 as read along with 7 people and 2 groups chad_davis barry pansapiens bicko sriram_s cjeans sobolevnrm 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 obligate-transient interactions by marti on 2008-04-30 15:32:42 as *** along with 4 people allmensch bicko chad_davis balicea
  • 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 obligate-transient interfaces interactions by marti on 2008-04-29 14:10:54 as read along with 3 people jteyra bicko choonpeng
  • 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 higueruelo bicko chad_davis choonpeng hmk
  • 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 prediction interfaces 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 measure conservation by marti on 2008-04-24 13:36:08 as read along with 1 person nklee
  • 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 svm prediction interfaces by marti on 2008-04-24 13:31:08 as read along with 8 people OriginalLurch bicko sriram_s chaleil ameetsoni cjeans Evangelia phoenixzxl
  • 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 prediction interfaces docking 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 prediction interfaces 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 5 people and 1 group Auger aalibes setar chad_davis GustavoLacerda 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 higueruelo barry bjorns wiehe julianm bicko chad_davis cjeans Evangelia 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 11 people and 1 group higueruelo baaden bicko anita chad_davis dgront sriram_s ruvido cjeans Evangelia Pao-Yang 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 higueruelo karbak aalibes baaden bicko chad_davis
  • 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 higueruelo bicko chad_davis jlh64
  • 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 1 person drastic
  • Statistical analysis and prediction of protein-protein interfaces
    Proteins: Structure, Function, and Bioinformatics, Vol. 60, No. 3. (19 May 2005), pp. 353-366.
    by Andrew J Bordner, Ruben Abagyan
    posted to interfaces prediction by marti on 2008-01-28 17:06:30 as *** along with 6 people and 2 groups barry bicko lyongu ameetsoni cjeans Evangelia structural_bioinformatics Bioinformatics
  • Matt: Local Flexibility Aids Protein Multiple Structure Alignment.
    PLoS Comput Biol, Vol. 4, No. 1. (11 January 2008)
    by Matthew Menke, Bonnie Berger, Lenore Cowen
    posted to alignments flexibility structure by marti on 2008-01-28 17:04:59 as *** along with 2 people carlk dimka
  • Sequence comparison by sequence harmony identifies subtype-specific functional sites
    Nucleic Acids Research, Vol. 34, No. 22. (December 2006), pp. 6540-6548.
    by Pirovano, Walter, Feenstra, K Anton, Heringa, Jaap
    posted to interfaces by marti on 2008-01-25 13:56:16 as *** along with 2 people and 2 groups marcius sriram_s BioinfoCIPF SGU-CIPF
  • Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins.
    J Mol Biol, Vol. 307, No. 5. (13 April 2001), pp. 1487-1502.
    by R Landgraf, I Xenarios, D Eisenberg
    posted to clusters interfaces by marti on 2008-01-25 13:55:38 as read along with 6 people and 2 groups barry pansapiens sriram_s cjeans mingzhi Pao-Yang structural_bioinformatics Bioinformatics
  • MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.
    Nucleic Acids Res, Vol. 30, No. 14. (15 July 2002), pp. 3059-3066.
    by K Katoh, K Misawa, K Kuma, T Miyata
    posted to msa by marti on 2008-01-24 15:32:45 as * along with 5 people urgi treangen zmasek rabio timflutre
  • 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 alignments blast by marti on 2008-01-24 14:37:42 as ** along with 41 people and 5 groups granujilla benwei ashaytan 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 siebertm ichbins81 jofiel Thaverkamp shung hervelequere dbk-lab EisenLab T_lab biomedical-nlp Microbial-Ecology
  • The Modular Organization of Domain Structures: Insights into Protein–Protein Binding
    PLoS Computational Biology, Vol. 3, No. 12. (1 December 2007), e239.
    by Del, Pablo Carbonell
    posted to interfaces by marti on 2008-01-24 12:09:00 as read along with 9 people carlk bicko chad_davis choonpeng grahamc cjeans zwang niallhaslam biehl
  • Prediction of protein-protein interaction sites using patch analysis.
    J Mol Biol, Vol. 272, No. 1. (12 September 1997), pp. 133-143.
    by S Jones, JM Thornton
    posted to interactions patch prediction by marti on 2008-01-24 12:08:05 as read along with 1 person cjeans
  • The interface of protein-protein complexes: Analysis of contacts and prediction of interactions.
    Cell Mol Life Sci (15 December 2007)
    by R P Bahadur, M Zacharias
    posted to interactions interfaces prediction by marti on 2008-01-24 12:07:35 as read along with 1 person higueruelo
  • Computational methods for the prediction of protein interactions.
    Curr Opin Struct Biol, Vol. 12, No. 3. (June 2002), pp. 368-373.
    by A Valencia, F Pazos
    posted to interactions prediction by marti on 2008-01-24 12:07:17 as read along with 1 person eckart_bindewald
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