Predikin and PredikinDB: a computational framework for the prediction of protein kinase peptide specificity and an associated database of phosphorylation sites.

Abstract:

BACKGROUND:We have previously described an approach to predicting the substrate specificity of serine-threonine protein kinases. The method, named Predikin, identifies key conserved substrate-determining residues in the kinase catalytic domain that contact the substrate in the region of the phosphorylation site and so determine the sequence surrounding the phosphorylation site. Predikin was implemented originally as a web application written in Javascript. RESULTS:Here, we describe a new version of Predikin, completely revised and rewritten as a modular framework that provides multiple enhancements compared with the original. Predikin now consists of two components: (i) PredikinDB, a database of phosphorylation sites that links substrates to kinase sequences and (ii) a Perl module, which provides methods to classify protein kinases, reliably identify substrate-determining residues, generate scoring matrices and score putative phosphorylation sites in query sequences. The performance of Predikin as measured using receiver operator characteristic (ROC) graph analysis equals or surpasses that of existing comparable methods. The Predikin website has been redesigned to incorporate the new features. CONCLUSION:New features in Predikin include the use of SQL queries to PredikinDB to generate predictions, scoring of predictions, more reliable identification of substrate-determining residues and putative phosphorylation sites, extended options to handle protein kinase and substrate data and an improved web interface. The new features significantly enhance the ability of Predikin to analyse protein kinases and their substrates. Predikin is available at http://predikin.biosci.uq.edu.au.

journal_name

BMC Bioinformatics

journal_title

BMC bioinformatics

authors

Saunders NF,Brinkworth RI,Huber T,Kemp BE,Kobe B

doi

10.1186/1471-2105-9-245

subject

Has Abstract

pub_date

2008-05-26 00:00:00

pages

245

issn

1471-2105

pii

1471-2105-9-245

journal_volume

9

pub_type

杂志文章
  • An automatic method to calculate heart rate from zebrafish larval cardiac videos.

    abstract:BACKGROUND:Zebrafish is a widely used model organism for studying heart development and cardiac-related pathogenesis. With the ability of surviving without a functional circulation at larval stages, strong genetic similarity between zebrafish and mammals, prolific reproduction and optically transparent embryos, zebrafi...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-018-2166-6

    authors: Kang CP,Tu HC,Fu TF,Wu JM,Chu PH,Chang DT

    更新日期:2018-05-09 00:00:00

  • Meta-eQTL: a tool set for flexible eQTL meta-analysis.

    abstract:BACKGROUND:Increasing number of eQTL (Expression Quantitative Trait Loci) datasets facilitate genetics and systems biology research. Meta-analysis tools are in need to jointly analyze datasets of same or similar issue types to improve statistical power especially in trans-eQTL mapping. Meta-analysis framework is also n...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-014-0392-0

    authors: Di Narzo AF,Cheng H,Lu J,Hao K

    更新日期:2014-11-28 00:00:00

  • PhylDiag: identifying complex synteny blocks that include tandem duplications using phylogenetic gene trees.

    abstract:BACKGROUND:Extant genomes share regions where genes have the same order and orientation, which are thought to arise from the conservation of an ancestral order of genes during evolution. Such regions of so-called conserved synteny, or synteny blocks, must be precisely identified and quantified, as a prerequisite to bet...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-15-268

    authors: Lucas JM,Muffato M,Roest Crollius H

    更新日期:2014-08-08 00:00:00

  • Fast discovery and visualization of conserved regions in DNA sequences using quasi-alignment.

    abstract:BACKGROUND:Next Generation Sequencing techniques are producing enormous amounts of biological sequence data and analysis becomes a major computational problem. Currently, most analysis, especially the identification of conserved regions, relies heavily on Multiple Sequence Alignment and its various heuristics such as p...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-14-S11-S2

    authors: Nagar A,Hahsler M

    更新日期:2013-01-01 00:00:00

  • phyloXML: XML for evolutionary biology and comparative genomics.

    abstract:BACKGROUND:Evolutionary trees are central to a wide range of biological studies. In many of these studies, tree nodes and branches need to be associated (or annotated) with various attributes. For example, in studies concerned with organismal relationships, tree nodes are associated with taxonomic names, whereas tree b...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-10-356

    authors: Han MV,Zmasek CM

    更新日期:2009-10-27 00:00:00

  • Developing optimal input design strategies in cancer systems biology with applications to microfluidic device engineering.

    abstract:BACKGROUND:Mechanistic models are becoming more and more popular in Systems Biology; identification and control of models underlying biochemical pathways of interest in oncology is a primary goal in this field. Unfortunately the scarce availability of data still limits our understanding of the intrinsic characteristics...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-10-S12-S4

    authors: Menolascina F,Bellomo D,Maiwald T,Bevilacqua V,Ciminelli C,Paradiso A,Tommasi S

    更新日期:2009-10-15 00:00:00

  • The EnzymeTracker: an open-source laboratory information management system for sample tracking.

    abstract:BACKGROUND:In many laboratories, researchers store experimental data on their own workstation using spreadsheets. However, this approach poses a number of problems, ranging from sharing issues to inefficient data-mining. Standard spreadsheets are also error-prone, as data do not undergo any validation process. To overc...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-13-15

    authors: Triplet T,Butler G

    更新日期:2012-01-26 00:00:00

  • Systematic integration of experimental data and models in systems biology.

    abstract:BACKGROUND:The behaviour of biological systems can be deduced from their mathematical models. However, multiple sources of data in diverse forms are required in the construction of a model in order to define its components and their biochemical reactions, and corresponding parameters. Automating the assembly and use of...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-11-582

    authors: Li P,Dada JO,Jameson D,Spasic I,Swainston N,Carroll K,Dunn W,Khan F,Malys N,Messiha HL,Simeonidis E,Weichart D,Winder C,Wishart J,Broomhead DS,Goble CA,Gaskell SJ,Kell DB,Westerhoff HV,Mendes P,Paton NW

    更新日期:2010-11-29 00:00:00

  • Extended analysis of benchmark datasets for Agilent two-color microarrays.

    abstract:BACKGROUND:As part of its broad and ambitious mission, the MicroArray Quality Control (MAQC) project reported the results of experiments using External RNA Controls (ERCs) on five microarray platforms. For most platforms, several different methods of data processing were considered. However, there was no similar consid...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-8-371

    authors: Kerr KF

    更新日期:2007-10-03 00:00:00

  • mSpecs: a software tool for the administration and editing of mass spectral libraries in the field of metabolomics.

    abstract:BACKGROUND:Metabolome analysis with GC/MS has meanwhile been established as one of the "omics" techniques. Compound identification is done by comparison of the MS data with compound libraries. Mass spectral libraries in the field of metabolomics ought to connect the relevant mass traces of the metabolites to other rele...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-10-229

    authors: Thielen B,Heinen S,Schomburg D

    更新日期:2009-07-22 00:00:00

  • A computational diffusion model to study antibody transport within reconstructed tumor microenvironments.

    abstract:BACKGROUND:Antibodies revolutionized cancer treatment over the past decades. Despite their successfully application, there are still challenges to overcome to improve efficacy, such as the heterogeneous distribution of antibodies within tumors. Tumor microenvironment features, such as the distribution of tumor and othe...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-020-03854-2

    authors: Cartaxo AL,Almeida J,Gualda EJ,Marsal M,Loza-Alvarez P,Brito C,Isidro IA

    更新日期:2020-11-17 00:00:00

  • Evaluation of methods for differential expression analysis on multi-group RNA-seq count data.

    abstract:BACKGROUND:RNA-seq is a powerful tool for measuring transcriptomes, especially for identifying differentially expressed genes or transcripts (DEGs) between sample groups. A number of methods have been developed for this task, and several evaluation studies have also been reported. However, those evaluations so far have...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-015-0794-7

    authors: Tang M,Sun J,Shimizu K,Kadota K

    更新日期:2015-11-04 00:00:00

  • SIMAT: GC-SIM-MS data analysis tool.

    abstract:BACKGROUND:Gas chromatography coupled with mass spectrometry (GC-MS) is one of the technologies widely used for qualitative and quantitative analysis of small molecules. In particular, GC coupled to single quadrupole MS can be utilized for targeted analysis by selected ion monitoring (SIM). However, to our knowledge, t...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-015-0681-2

    authors: Ranjbar MR,Di Poto C,Wang Y,Ressom HW

    更新日期:2015-08-19 00:00:00

  • CLU: a new algorithm for EST clustering.

    abstract:BACKGROUND:The continuous flow of EST data remains one of the richest sources for discoveries in modern biology. The first step in EST data mining is usually associated with EST clustering, the process of grouping of original fragments according to their annotation, similarity to known genomic DNA or each other. Cluste...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-6-S2-S3

    authors: Ptitsyn A,Hide W

    更新日期:2005-07-15 00:00:00

  • Evaluation of gene-expression clustering via mutual information distance measure.

    abstract:BACKGROUND:The definition of a distance measure plays a key role in the evaluation of different clustering solutions of gene expression profiles. In this empirical study we compare different clustering solutions when using the Mutual Information (MI) measure versus the use of the well known Euclidean distance and Pears...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-8-111

    authors: Priness I,Maimon O,Ben-Gal I

    更新日期:2007-03-30 00:00:00

  • Googling DNA sequences on the World Wide Web.

    abstract:BACKGROUND:New web-based technologies provide an excellent opportunity for sharing and accessing information and using web as a platform for interaction and collaboration. Although several specialized tools are available for analyzing DNA sequence information, conventional web-based tools have not been utilized for bio...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-10-S14-S4

    authors: Hajibabaei M,Singer GA

    更新日期:2009-11-10 00:00:00

  • MetaMIS: a metagenomic microbial interaction simulator based on microbial community profiles.

    abstract:BACKGROUND:The complexity and dynamics of microbial communities are major factors in the ecology of a system. With the NGS technique, metagenomics data provides a new way to explore microbial interactions. Lotka-Volterra models, which have been widely used to infer animal interactions in dynamic systems, have recently ...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-016-1359-0

    authors: Shaw GT,Pao YY,Wang D

    更新日期:2016-11-25 00:00:00

  • The reactive metabolite target protein database (TPDB)--a web-accessible resource.

    abstract:BACKGROUND:The toxic effects of many simple organic compounds stem from their biotransformation to chemically reactive metabolites which bind covalently to cellular proteins. To understand the mechanisms of cytotoxic responses it may be important to know which proteins become adducted and whether some may be common tar...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-8-95

    authors: Hanzlik RP,Koen YM,Theertham B,Dong Y,Fang J

    更新日期:2007-03-16 00:00:00

  • FastGroup: a program to dereplicate libraries of 16S rDNA sequences.

    abstract:BACKGROUND:Ribosomal 16S DNA sequences are an essential tool for identifying and classifying microbes. High-throughput DNA sequencing now makes it economically possible to produce very large datasets of 16S rDNA sequences in short time periods, necessitating new computer tools for analyses. Here we describe FastGroup, ...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-2-9

    authors: Seguritan V,Rohwer F

    更新日期:2001-01-01 00:00:00

  • The InDeVal insertion/deletion evaluation tool: a program for finding target regions in DNA sequences and for aiding in sequence comparison.

    abstract:BACKGROUND:The program InDeVal was originally developed to help researchers find known regions of insertion/deletion activity (with the exception of isolated single-base indels) in newly determined Poaceae trnL-F sequences and compare them with 533 previously determined sequences. It is supplied with input files design...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-5-173

    authors: Stoneberg Holt SD,Holt JA

    更新日期:2004-10-29 00:00:00

  • Ontology driven integration platform for clinical and translational research.

    abstract::Semantic Web technologies offer a promising framework for integration of disparate biomedical data. In this paper we present the semantic information integration platform under development at the Center for Clinical and Translational Sciences (CCTS) at the University of Texas Health Science Center at Houston (UTHSC-H)...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-10-S2-S2

    authors: Mirhaji P,Zhu M,Vagnoni M,Bernstam EV,Zhang J,Smith JW

    更新日期:2009-02-05 00:00:00

  • Multi-view feature selection for identifying gene markers: a diversified biological data driven approach.

    abstract:BACKGROUND:In recent years, to investigate challenging bioinformatics problems, the utilization of multiple genomic and proteomic sources has become immensely popular among researchers. One such issue is feature or gene selection and identifying relevant and non-redundant marker genes from high dimensional gene express...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-020-03810-0

    authors: Acharya S,Cui L,Pan Y

    更新日期:2020-12-30 00:00:00

  • LSX: automated reduction of gene-specific lineage evolutionary rate heterogeneity for multi-gene phylogeny inference.

    abstract:BACKGROUND:Lineage rate heterogeneity can be a major source of bias, especially in multi-gene phylogeny inference. We had previously tackled this issue by developing LS3, a data subselection algorithm that, by removing fast-evolving sequences in a gene-specific manner, identifies subsets of sequences that evolve at a r...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-019-3020-1

    authors: Rivera-Rivera CJ,Montoya-Burgos JI

    更新日期:2019-08-13 00:00:00

  • Prediction of heart disease and classifiers' sensitivity analysis.

    abstract:BACKGROUND:Heart disease (HD) is one of the most common diseases nowadays, and an early diagnosis of such a disease is a crucial task for many health care providers to prevent their patients for such a disease and to save lives. In this paper, a comparative analysis of different classifiers was performed for the classi...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-020-03626-y

    authors: Almustafa KM

    更新日期:2020-07-02 00:00:00

  • MACSIMS: multiple alignment of complete sequences information management system.

    abstract:BACKGROUND:In the post-genomic era, systems-level studies are being performed that seek to explain complex biological systems by integrating diverse resources from fields such as genomics, proteomics or transcriptomics. New information management systems are now needed for the collection, validation and analysis of the...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-7-318

    authors: Thompson JD,Muller A,Waterhouse A,Procter J,Barton GJ,Plewniak F,Poch O

    更新日期:2006-06-23 00:00:00

  • SSWAP: A Simple Semantic Web Architecture and Protocol for semantic web services.

    abstract:BACKGROUND:SSWAP (Simple Semantic Web Architecture and Protocol; pronounced "swap") is an architecture, protocol, and platform for using reasoning to semantically integrate heterogeneous disparate data and services on the web. SSWAP was developed as a hybrid semantic web services technology to overcome limitations foun...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-10-309

    authors: Gessler DD,Schiltz GS,May GD,Avraham S,Town CD,Grant D,Nelson RT

    更新日期:2009-09-23 00:00:00

  • The Korean Bird Information System (KBIS) through open and public participation.

    abstract:BACKGROUND:The importance of biodiversity conservation has been increasing steadily due to its benefits to human beings. Recently, producing and managing biodiversity databases have become much easier because of the information technology (IT) advancement. This made the general public's participation in biodiversity co...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-10-S15-S11

    authors: Paik IH,Lim J,Chun BS,Jin SD,Yu JP,Lee JW,Bhak J,Paek WK

    更新日期:2009-12-03 00:00:00

  • Bioinformatics approach to predict target genes for dysregulated microRNAs in hepatocellular carcinoma: study on a chemically-induced HCC mouse model.

    abstract:BACKGROUND:Hepatocellular carcinoma (HCC) is an aggressive epithelial tumor which shows very poor prognosis and high rate of recurrence, representing an urgent problem for public healthcare. MicroRNAs (miRNAs/miRs) are a class of small, non-coding RNAs that attract great attention because of their role in regulation of...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-015-0836-1

    authors: Del Vecchio F,Gallo F,Di Marco A,Mastroiaco V,Caianiello P,Zazzeroni F,Alesse E,Tessitore A

    更新日期:2015-12-10 00:00:00

  • An automated framework for understanding structural variations in the binding grooves of MHC class II molecules.

    abstract:BACKGROUND:MHC/HLA class II molecules are important components of the immune system and play a critical role in processes such as phagocytosis. Understanding peptide recognition properties of the hundreds of MHC class II alleles is essential to appreciate determinants of antigenicity and ultimately to predict epitopes....

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-11-S1-S55

    authors: Yeturu K,Utriainen T,Kemp GJ,Chandra N

    更新日期:2010-01-18 00:00:00

  • GOPET: a tool for automated predictions of Gene Ontology terms.

    abstract:BACKGROUND:Vast progress in sequencing projects has called for annotation on a large scale. A Number of methods have been developed to address this challenging task. These methods, however, either apply to specific subsets, or their predictions are not formalised, or they do not provide precise confidence values for th...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-7-161

    authors: Vinayagam A,del Val C,Schubert F,Eils R,Glatting KH,Suhai S,König R

    更新日期:2006-03-20 00:00:00