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neils's prediction [52 articles]

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  • Revisiting the Saccharomyces cerevisiae predicted ORFeome
    Genome Res. (2008)
    by Qian R Li, Anne R Carvunis, Haiyuan Yu, Jing, Quan Zhong, Nicolas Simonis, Stanley Tam, Tong Hao, Niels J Klitgord, Denis Dupuy, Danny Mou, Ilan Wapinski, Aviv Regev, David E Hill, Michael E Cusick, Marc Vidal
    posted to orfan transcript yeast prediction orfs genomics by neils on 2008-07-11 04:48:06 as **
  • Extracting sequence features to predict protein-DNA interactions: a comparative study
    Nucl. Acids Res., Vol. 36, No. 12. (1 July 2008), pp. 4137-4148.
    by Qing Zhou, Jun S Liu
    posted to sequence protein-dna prediction interaction bioinformatics by neils on 2008-07-11 00:31:23 as **
  • InteroPorc: Automated Inference of Highly Conserved Protein Interaction Networks.
    Bioinformatics (Oxford, England) (28 May 2008)
    by Magali Michaut, Samuel Kerrien, Luisa Montecchi-Palazzi, Franck Chauvat, Corinne Cassier-Chauvat, Jean-Christophe C Aude, Pierre Legrain
    posted to network protein-protein prediction interaction bioinformatics by neils on 2008-07-07 14:13:12 as ** along with 2 people renatomilani cabbagesofdoom
  • Global investigation of protein-protein interactions in yeast Saccharomyces cerevisiae using re-occurring short polypeptide sequences
    Nucl. Acids Res. (27 June 2008), gkn390.
    by S Pitre, C North, M Alamgir, M Jessulat, A Chan, X Luo, JR Green, M Dumontier, F Dehne, A Golshani
    posted to peptide yeast protein-protein prediction interaction bioinformatics by neils on 2008-06-28 03:28:18 as ** along with 3 people renatomilani brianb pansapiens
  • Inferring modules of functionally interacting proteins using the Bond Energy Algorithm.
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Ryosuke Watanabe, Enrique Morett, Edgar Vallejo
    posted to algorithm protein-protein prediction interaction energy by neils on 2008-06-18 00:57:15 as **
  • PURE: a webserver for the prediction of domains in unassigned regions in proteins
    BMC Bioinformatics, Vol. 9 (14 June 2008), 281.
    by Chilamakuri CS Reddy, Shameer Khader, Bernard O Offmann, Ramanthan Sowdhamini
    posted to region webserver protein prediction domain bioinformatics by neils on 2008-06-15 10:50:02 as ** along with 1 person niallhaslam
  • PhosphoScan: A Probability-Based Method for Phosphorylation Site Prediction Using MS2/MS3 Pair Information
    J. Proteome Res. (13 June 2008)
    by Yunhu Wan, Diane Cripps, Stefani Thomas, Patricia Campbell, Nicholas Ambulos, Ting Chen, Austin Yang
    posted to mass-spec probability prediction phosphorylation by neils on 2008-06-13 14:53:58 as **
  • The protein structure prediction problem could be solved using the current PDB library.
    Proc Natl Acad Sci U S A, Vol. 102, No. 4. (25 January 2005), pp. 1029-1034.
    by Y Zhang, J Skolnick
    posted to structure protein prediction pdb modelling homology casp by neils on 2008-06-12 07:42:10 as ** along with 9 people and 3 groups karbak iakes vavi marcius alexg j3xucite kracher schuylrp jfmuggs BioinfoCIPF Immunoinformatics SGU-CIPF
  • Large-scale analysis of gene clustering in bacteria
    Genome Res., Vol. 18, No. 6. (1 June 2008), pp. 949-956.
    by Qingwu Yang, Sing-Hoi Sze
    posted to prediction operon genetics clustering bioinformatics bacteria by neils on 2008-06-03 02:29:35 as **
  • poolHiTS: A Shifted Transversal Design based pooling strategy for high-throughput drug screening
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Raghunandan Kainkaryam, Peter Woolf
    posted to screen prediction drug bioinformatics by neils on 2008-05-31 03:53:47 as ** along with 2 people jyuh reyez
  • PIE: an online prediction system for protein-protein interactions from text
    Nucl. Acids Res. (28 May 2008), gkn281.
    by Sun Kim, Soo-Yong Shin, In-Hee Lee, Soo-Jin Kim, Ram Sriram, Byoung-Tak Zhang
    posted to webserver text-mining protein-protein prediction interaction bioinformatics by neils on 2008-05-29 03:02:27 as ** along with 1 person tharris
  • Prediction of enzyme function by combining sequence similarity and protein interactions
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Jordi Espadaler, Narayanan Eswar, Enric Querol, Francesc Aviles, Andrej Sali, Marc M Renom, Baldomero Oliva
    posted to sequence protein-protein prediction interaction function enzyme bioinformatics by neils on 2008-05-28 01:05:07 as **
  • Predikin and PredikinDB: a computational framework for the prediction of protein kinase peptide specificity and an associated database of phosphorylation sites
    BMC Bioinformatics, Vol. 9 (26 May 2008), 245.
    by Neil FW Saunders, Ross I Brinkworth, Thomas Huber, Bruce E Kemp, Bostjan Kobe
    posted to kinase substrate specificity predikin prediction bioinformatics by neils on 2008-05-27 05:06:18 as **
  • Estimating the size of the human interactome
    Proceedings of the National Academy of Sciences (12 May 2008), 0708078105.
    by Michael P Stumpf, Thomas Thorne, Eric de Silva, Ronald Stewart, Hyeong J An, Michael Lappe, Carsten Wiuf
    posted to protein-protein prediction network interactome interaction human bioinformatics by neils on 2008-05-14 04:39:31 as ** along with 18 people chad_davis Evangelia balicea marck paolomarcatili sanchezbuelna cabbagesofdoom xingxu mjoach jyuh chrissp100 zwang roys brianb friendpine Ema tmmurali phoenixzxl
  • The Predikin webserver: improved prediction of protein kinase peptide specificity using structural information
    Nucl. Acids Res. (13 May 2008), gkn279.
    by Neil F Saunders, Bostjan Kobe
    posted to kinase webserver specificity predikin prediction peptide bioinformatics by neils on 2008-05-14 03:57:42 as **
  • Biocomputational prediction of small non-coding RNAs in Streptomyces
    BMC Genomics, Vol. 9, No. 1. (2008)
    by Josef Panek, Jan Bobek, Karel Mikulik, Marek Basler, Jiri Vohradsky
    posted to streptomyces prediction ncrna bioinformatics bacteria by neils on 2008-05-13 13:09:48 as **
  • Predicted roles for hypothetical proteins in the low-temperature expressed proteome of the Antarctic archaeon Methanococcoides burtonii.
    Journal of proteome research, Vol. 4, No. 2. (r 2005), pp. 464-472.
    by NF Saunders, A Goodchild, M Raftery, M Guilhaus, PM Curmi, R Cavicchioli
    posted to protein psychrophily prediction methanococcoides function bioinformatics archaea antarctic by neils on 2008-05-11 10:09:25 as **
  • Fast protein tertiary structure retrieval based on global surface shape similarity
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (xx 2008)
    by Lee Sael, Bin Li, David La, Yi Fang, Karthik Ramani, Raif Rustamov, Daisuke Kihara
    posted to structure retrieval protein prediction bioinformatics by neils on 2008-05-09 10:19:56 as **
  • SCPRED: Accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Lukasz Kurgan, Krzysztof Cios, Ke Chen
    posted to structure sequence protein prediction bioinformatics by neils on 2008-05-02 00:27:57 as **
  • 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 structure protein prediction modelling homology evaluation bioinformatics by neils on 2008-04-26 12:05:56 as ** along with 3 people pansapiens chad_davis biehl
  • Constructing templates for protein structure prediction by simulation of protein folding pathways
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by Ilona Kifer, Ruth Nussinov, Haim J Wolfson
    posted to structure simulation protein prediction modelling folding by neils on 2008-04-25 01:52:40 as **
  • NetworKIN: a resource for exploring cellular phosphorylation networks
    Nucl. Acids Res., Vol. 36 (2008), pp. D695-699.
    by Rune Linding, Lars J Jensen, Adrian Pasculescu, Marina Olhovsky, Karen Colwill, Peer Bork, Michael B Yaffe, Tony Pawson
    posted to network transduction signal prediction phosphorylation bioinformatics by neils on 2008-04-24 16:22:01 as **
  • Genome-wide subcellular localization of putative outer membrane and extracellular proteins in Leptospira interrogans serovar Lai genome using bioinformatics approaches
    BMC Genomics, Vol. 9, No. 1. (2008)
    by Wasna Viratyosin, Supawadee Ingsriswang, Eakasit Pacharawongsakda, Prasit Palittapongarnpim
    posted to bacteria bioinformatics genomics leptospira localisation membrane pathogen prediction protein scl secretion by neils on 2008-04-21 05:05:55 as ** along with 1 person sitake
  • Functional Maps of Protein Complexes from Quantitative Genetic Interaction Data
    PLoS Comput Biol, Vol. 4, No. 4. (Apr 2008)
    by Sourav Bandyopadhyay, Ryan Kelley, Nevan J Krogan, Trey Ideker
    posted to network complex genetics bioinformatics interaction prediction protein-protein by neils on 2008-04-21 03:13:52 as **
  • Predicting Co-Complexed Protein Pairs from Heterogeneous Data
    PLoS Comput Biol, Vol. 4, No. 4. (Apr 2008)
    by Jian Qiu, William S Noble
    posted to kernel complex bioinformatics interaction prediction protein-protein by neils on 2008-04-21 03:12:15 as ** along with 1 person brianb
  • Indicators from archaeal secretomes.
    Microbiological research (11 April 2008)
    by Mazen Saleh, Catharine Song, Sabah Nasserulla, L G G Leduc
    posted to analysis archaea bioinformatics genomics prediction secretion by neils on 2008-04-18 12:25:45 as **
  • Identification of Proteins Secreted by Malaria Parasite into Erythrocyte using SVM and PSSM profiles
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Ruchi Verma, Ajit Tiwari, Sukhwinder Kaur, Grish Varshney, Gajendra Raghava
    posted to protein bioinformatics erythrocyte machine-learning malaria prediction pssm secretion svm by neils on 2008-04-17 00:31:17 as ** along with 1 person arNQ
  • Identification of Phosphorylation Sites in Protein Kinase A Substrates Using Artificial Neural Networks and Mass Spectrometry
    J. Proteome Res., Vol. 3, No. 3. (14 June 2004), pp. 426-433.
    by M Hjerrild, A Stensballe, TE Rasmussen, CB Kofoed, N Blom, T Sicheritz-Ponten, MR Larsen, S Brunak, ON Jensen, S Gammeltoft
    posted to mass-spec article-predikin bioinformatics netphosk neural-network phosphorylation prediction by neils on 2008-04-16 04:05:30 as **
  • A Systematic Assessment of MHC Class II Peptide Binding Predictions and Evaluation of a Consensus Approach
    PLoS Comput Biol, Vol. 4, No. 4. (Apr 2008)
    by Peng Wang, John Sidney, Courtney Dow, Bianca Mothé, Alessandro Sette, Bjoern Peters
    posted to affinity binding bioinformatics evaluation mhc peptide prediction by neils on 2008-04-15 03:01:11 as **
  • Ligand binding affinity prediction by linear interaction energy methods
    Journal of Computer-Aided Molecular Design, Vol. 12, No. 1. (1 January 1998), pp. 27-35.
    by Tomas Hansson, John Marelius, Johan Åqvist
    posted to affinity binding bioinformatics lie ligand prediction by neils on 2008-04-15 02:18:54 as **
  • LocateP: Genome-scale subcellular-location predictor for bacterial proteins
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Miaomiao Zhou, Jos Boekhorst, Christof Francke, Roland Siezen
    posted to bacteria bioinformatics genomics localisation prediction scl subcellular by neils on 2008-03-27 23:16:35 as **
  • ParCrys: a Parzen window density estimation approach to protein crystallization propensity prediction
    Bioinformatics, Vol. 24, No. 7. (1 April 2008), pp. 901-907.
    by Ian M Overton, Gianandrea Padovani, Mark A Girolami, Geoffrey J Barton
    posted to structural-genomics bioinformatics crystallography prediction propensity protein by neils on 2008-03-26 23:39:33 as **
  • PSLDoc: Protein subcellular localization prediction based on gapped-dipeptides and probabilistic latent semantic analysis.
    Proteins (7 February 2008)
    by Jia-Ming M Chang, Emily Chia-Yu C Su, Allan Lo, Hua-Sheng S Chiu, Ting-Yi Y Sung, Wen-Lian L Hsu
    posted to bioinformatics localisation prediction scl semantic subcellular by neils on 2008-03-26 02:26:32 as **
  • Meta-prediction of phosphorylation sites with weighted voting and restricted grid search parameter selection.
    Nucleic Acids Res, Vol. 36, No. 4. (March 2008)
    by J Wan, S Kang, C Tang, J Yan, Y Ren, J Liu, X Gao, A Banerjee, LB Ellis, T Li
    posted to bioinformatics meta-prediction phosphorylation prediction by neils on 2008-03-10 07:23:25 as **
  • Structure-based prediction of transcription factor binding sites using a protein-DNA docking approach
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by Zhijie Liu, Jun-Tao Guo, Ting Li, Ying Xu
    posted to factors binding bioinformatics docking prediction structure transcription by neils on 2008-03-05 01:15:12 as ** along with 1 person aalibes
  • Efficient peptide-MHC-I binding prediction for alleles with few known binders
    Bioinformatics, Vol. 24, No. 3. (1 February 2008), pp. 358-366.
    by Laurent Jacob, Jean-Philippe Vert
    posted to peptide allele bioinformatics mhc prediction by neils on 2008-01-31 11:22:31 as **
  • A computational approach for detecting peptidases and their specific inhibitors at the genome level.
    BMC Bioinformatics, Vol. 8 Suppl 1 (2007)
    by L Bartoli, R Calabrese, P Fariselli, DG Mita, R Casadio
    posted to inhibitor bioinformatics interaction peptidase prediction protein-protein by neils on 2008-01-28 07:31:30 as **
  • Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain.
    PLoS Comput Biol, Vol. 2, No. 1. (January 2006)
    by T Hou, K Chen, WA McLaughlin, B Lu, W Wang
    posted to abl bioinformatics domain interaction prediction protein-protein sh3 by neils on 2008-01-24 08:10:57 as ** along with 3 people carlescorbi Evangelia biehl
  • Enhancing the prediction of protein pairings between interacting families using orthology information
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Jose Izarzugaza, David Juan, Carles Pons, Florencio Pazos, Alfonso Valencia
    posted to bioinformatics interaction orthology phylogeny prediction protein-protein by neils on 2008-01-24 02:01:55 as ** along with 1 person chad_davis
  • Accurate structural correlations from maximum likelihood superpositions
    PLoS Computational Biology, Vol. preprint, No. 2008. (1 January 2008), e43.eor.
    by Douglas L Theobald, Deborah S Wuttke
    posted to md nmr pca prediction structure by neils on 2008-01-17 23:48:31 as **
  • Conformational Switching upon Phosphorylation: A Predictive Framework Based on Energy Landscape Principles
    Biochemistry (17 January 2008)
    by J Latzer, T Shen, PG Wolynes
    posted to energy phosphorylation prediction structure by neils on 2008-01-17 23:36:50 as ** along with 2 people and 1 group sobolevnrm paulschlesinger baker-group
  • Prediction of enzyme function based on 3D templates of evolutionarily important amino acids
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by David Kristensen, Matthew R Ward, Andreas M Lisewski, Serkan Erdin, Brian Chen, Viacheslav Fofanov, Marek Kimmel, Lydia Kavraki, Olivier Lichtarge
    posted to enzyme bioinformatics function prediction structure by neils on 2008-01-12 01:38:13 as ** along with 1 person and 1 group sobolevnrm baker-group
  • Inferring domain-domain interactions from protein-protein interactions.
    Genome Res, Vol. 12, No. 10. (October 2002), pp. 1540-1548.
    by M Deng, S Mehta, F Sun, T Chen
    posted to domain bioinformatics interaction prediction by neils on 2008-01-10 05:26:02 as ** along with 6 people carlk maryee opheliav wnpx Pao-Yang phoenixzxl
  • Enhanced Membrane Protein Topology Prediction Using a Hierarchical Classification Method and a New Scoring Function
    J. Proteome Res. (15 December 2007)
    by Allan Lo, Hua-Sheng Chiu, Ting-Yi Sung, Ping-Chiang Lyu, Wen-Lian Hsu
    posted to protein bioinformatics membrane prediction svm by neils on 2007-12-15 07:22:26 as **
  • Predicting gene ontology functions from protein's regional surface structures
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Zhi P Liu, Ling Y Wu, Yong Wang, Luonan Chen, Xiang S Zhang
    posted to protein function ontology prediction structure by neils on 2007-12-11 06:25:59 as ** along with 2 people carlk tjimenez
  • Analyzing protein function on a genomic scale: the importance of gold-standard positives and negatives for network prediction.
    Curr Opin Microbiol, Vol. 7, No. 5. (October 2004), pp. 535-545.
    by R Jansen, M Gerstein
    posted to network protein bioinformatics prediction by neils on 2007-12-10 00:09:13 as ** along with 5 people and 2 groups carlk okarsligil lfriedl wnpx grahamc kdl Bioinformatics
  • Computational methods for protein-protein interaction and their application.
    Curr Protein Pept Sci, Vol. 6, No. 5. (October 2005), pp. 443-449.
    by TL Shi, YX Li, YD Cai, KC Chou
    posted to network protein bioinformatics interaction prediction by neils on 2007-12-10 00:07:11 as ** along with 1 person bicko
  • Refining Protein Subcellular Localization
    PLoS Computational Biology, Vol. 1, No. 6. (1 November 2005), e66.
    by Michelle S Scott, Sara J Calafell, David Y Thomas, Michael T Hallett
    posted to protein bioinformatics localisation prediction subcellular by neils on 2007-12-07 08:36:11 as ** along with 2 people and 1 group dolhuis grahamc SNE
  • A new computational approach to analyze human protein complexes and predict novel protein interactions
    Genome Biology, Vol. 8, No. 12. (2007)
    by Sara Zanivan, Ilaria Cascone, Chiara Peyron, Ivan Molineris, Serena Marchio, Michele Caselle, Federico Bussolino
    posted to bioinformatics interaction kinase p21-activated prediction protein by neils on 2007-12-05 01:24:31 as ** along with 2 people grahamc barriot
  • Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Takeyuki Tamura, Tatsuya Akutsu
    posted to bioinformatics prediction scl by neils on 2007-11-30 01:59:12 as ** along with 2 people mdstobbe grahamc
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