ProLego: tool for extracting and visualizing topological modules in protein structures.


BACKGROUND:In protein design, correct use of topology is among the initial and most critical feature. Meticulous selection of backbone topology aids in drastically reducing the structure search space. With ProLego, we present a server application to explore the component aspect of protein structures and provide an intuitive and efficient way to scan the protein topology space. RESULT:We have implemented in-house developed "topological representation" in an automated-pipeline to extract protein topology from given protein structure. Using the topology string, ProLego, compares topology against a non-redundant extensive topology database (ProLegoDB) as well as extracts constituent topological modules. The platform offers interactive topology visualization graphs. CONCLUSION:ProLego, provides an alternative but comprehensive way to scan and visualize protein topology along with an extensive database of protein topology. ProLego can be found at


BMC Bioinformatics


BMC bioinformatics


Khan T,Panday SK,Ghosh I




Has Abstract


2018-05-04 00:00:00












  • Widespread evidence of viral miRNAs targeting host pathways.

    abstract:BACKGROUND:MicroRNAs (miRNA) are regulatory genes that target and repress other RNA molecules via sequence-specific binding. Several biological processes are regulated across many organisms by evolutionarily conserved miRNAs. Plants and invertebrates employ their miRNA in defense against viruses by targeting and degrad...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Carl JW Jr,Trgovcich J,Hannenhalli S

    更新日期:2013-01-01 00:00:00

  • Use of a structural alphabet for analysis of short loops connecting repetitive structures.

    abstract:BACKGROUND:Because loops connect regular secondary structures, analysis of the former depends directly on the definition of the latter. The numerous assignment methods, however, can offer different definitions. In a previous study, we defined a structural alphabet composed of 16 average protein fragments, which we call...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Fourrier L,Benros C,de Brevern AG

    更新日期:2004-05-12 00:00:00

  • DART: Denoising Algorithm based on Relevance network Topology improves molecular pathway activity inference.

    abstract:BACKGROUND:Inferring molecular pathway activity is an important step towards reducing the complexity of genomic data, understanding the heterogeneity in clinical outcome, and obtaining molecular correlates of cancer imaging traits. Increasingly, approaches towards pathway activity inference combine molecular profiles (...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Jiao Y,Lawler K,Patel GS,Purushotham A,Jones AF,Grigoriadis A,Tutt A,Ng T,Teschendorff AE

    更新日期:2011-10-19 00:00:00

  • EGNAS: an exhaustive DNA sequence design algorithm.

    abstract:BACKGROUND:The molecular recognition based on the complementary base pairing of deoxyribonucleic acid (DNA) is the fundamental principle in the fields of genetics, DNA nanotechnology and DNA computing. We present an exhaustive DNA sequence design algorithm that allows to generate sets containing a maximum number of seq...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Kick A,Bönsch M,Mertig M

    更新日期:2012-06-20 00:00:00

  • Quantitative prediction of the effect of genetic variation using hidden Markov models.

    abstract:BACKGROUND:With the development of sequencing technologies, more and more sequence variants are available for investigation. Different classes of variants in the human genome have been identified, including single nucleotide substitutions, insertion and deletion, and large structural variations such as duplications and...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Liu M,Watson LT,Zhang L

    更新日期:2014-01-09 00:00:00

  • Inferring the role of transcription factors in regulatory networks.

    abstract:BACKGROUND:Expression profiles obtained from multiple perturbation experiments are increasingly used to reconstruct transcriptional regulatory networks, from well studied, simple organisms up to higher eukaryotes. Admittedly, a key ingredient in developing a reconstruction method is its ability to integrate heterogeneo...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Veber P,Guziolowski C,Le Borgne M,Radulescu O,Siegel A

    更新日期:2008-05-06 00:00:00

  • An improved classification of G-protein-coupled receptors using sequence-derived features.

    abstract:BACKGROUND:G-protein-coupled receptors (GPCRs) play a key role in diverse physiological processes and are the targets of almost two-thirds of the marketed drugs. The 3 D structures of GPCRs are largely unavailable; however, a large number of GPCR primary sequences are known. To facilitate the identification and charact...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Peng ZL,Yang JY,Chen X

    更新日期:2010-08-09 00:00:00

  • Pre-processing Agilent microarray data.

    abstract:BACKGROUND:Pre-processing methods for two-sample long oligonucleotide arrays, specifically the Agilent technology, have not been extensively studied. The goal of this study is to quantify some of the sources of error that affect measurement of expression using Agilent arrays and to compare Agilent's Feature Extraction ...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Zahurak M,Parmigiani G,Yu W,Scharpf RB,Berman D,Schaeffer E,Shabbeer S,Cope L

    更新日期:2007-05-01 00:00:00

  • A Web-based and Grid-enabled dChip version for the analysis of large sets of gene expression data.

    abstract:BACKGROUND:Microarray techniques are one of the main methods used to investigate thousands of gene expression profiles for enlightening complex biological processes responsible for serious diseases, with a great scientific impact and a wide application area. Several standalone applications had been developed in order t...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Corradi L,Fato M,Porro I,Scaglione S,Torterolo L

    更新日期:2008-11-13 00:00:00

  • Optimizing agent-based transmission models for infectious diseases.

    abstract:BACKGROUND:Infectious disease modeling and computational power have evolved such that large-scale agent-based models (ABMs) have become feasible. However, the increasing hardware complexity requires adapted software designs to achieve the full potential of current high-performance workstations. RESULTS:We have found l...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Willem L,Stijven S,Tijskens E,Beutels P,Hens N,Broeckhove J

    更新日期:2015-06-02 00:00:00

  • Hit integration for identifying optimal spaced seeds.

    abstract:BACKGROUND:Introduction of spaced speeds opened a way of sensitivity improvement in homology search without loss of search speed. Since then, the efforts of finding optimal seed which maximizes the sensitivity have been continued today. The sensitivity of a seed is generally computed by its hit probability. However, th...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Chung WH,Park SB

    更新日期:2010-01-18 00:00:00

  • Pripper: prediction of caspase cleavage sites from whole proteomes.

    abstract:BACKGROUND:Caspases are a family of proteases that have central functions in programmed cell death (apoptosis) and inflammation. Caspases mediate their effects through aspartate-specific cleavage of their target proteins, and at present almost 400 caspase substrates are known. There are several methods developed to pre...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Piippo M,Lietzén N,Nevalainen OS,Salmi J,Nyman TA

    更新日期:2010-06-15 00:00:00

  • Asymmetric bagging and feature selection for activities prediction of drug molecules.

    abstract:BACKGROUND:Activities of drug molecules can be predicted by QSAR (quantitative structure activity relationship) models, which overcomes the disadvantages of high cost and long cycle by employing the traditional experimental method. With the fact that the number of drug molecules with positive activity is rather fewer t...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Li GZ,Meng HH,Lu WC,Yang JY,Yang MQ

    更新日期:2008-05-28 00:00:00

  • Venn-diaNet : venn diagram based network propagation analysis framework for comparing multiple biological experiments.

    abstract:BACKGROUND:The main research topic in this paper is how to compare multiple biological experiments using transcriptome data, where each experiment is measured and designed to compare control and treated samples. Comparison of multiple biological experiments is usually performed in terms of the number of DEGs in an arbi...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Hur B,Kang D,Lee S,Moon JH,Lee G,Kim S

    更新日期:2019-12-27 00:00:00

  • Qxpak.5: old mixed model solutions for new genomics problems.

    abstract:BACKGROUND:Mixed models have a long and fruitful history in statistics. They are pertinent to genomics problems because they are highly versatile, accommodating a wide variety of situations within the same theoretical and algorithmic framework. RESULTS:Qxpak is a package for versatile statistical genomics, specificall...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Pérez-Enciso M,Misztal I

    更新日期:2011-05-25 00:00:00

  • MGOGP: a gene module-based heuristic algorithm for cancer-related gene prioritization.

    abstract:BACKGROUND:Prioritizing genes according to their associations with a cancer allows researchers to explore genes in more informed ways. By far, Gene-centric or network-centric gene prioritization methods are predominated. Genes and their protein products carry out cellular processes in the context of functional modules....

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Su L,Liu G,Bai T,Meng X,Ma Q

    更新日期:2018-06-05 00:00:00

  • A unifying model of genome evolution under parsimony.

    abstract:BACKGROUND:Parsimony and maximum likelihood methods of phylogenetic tree estimation and parsimony methods for genome rearrangements are central to the study of genome evolution yet to date they have largely been pursued in isolation. RESULTS:We present a data structure called a history graph that offers a practical ba...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Paten B,Zerbino DR,Hickey G,Haussler D

    更新日期:2014-06-19 00:00:00

  • GlycomeDB - integration of open-access carbohydrate structure databases.

    abstract:BACKGROUND:Although carbohydrates are the third major class of biological macromolecules, after proteins and DNA, there is neither a comprehensive database for carbohydrate structures nor an established universal structure encoding scheme for computational purposes. Funding for further development of the Complex Carboh...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Ranzinger R,Herget S,Wetter T,von der Lieth CW

    更新日期:2008-09-19 00:00:00

  • A stochastic context free grammar based framework for analysis of protein sequences.

    abstract:BACKGROUND:In the last decade, there have been many applications of formal language theory in bioinformatics such as RNA structure prediction and detection of patterns in DNA. However, in the field of proteomics, the size of the protein alphabet and the complexity of relationship between amino acids have mainly limited...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Dyrka W,Nebel JC

    更新日期:2009-10-08 00:00:00

  • MRCQuant- an accurate LC-MS relative isotopic quantification algorithm on TOF instruments.

    abstract:BACKGROUND:Relative isotope abundance quantification, which can be used for peptide identification and differential peptide quantification, plays an important role in liquid chromatography-mass spectrometry (LC-MS)-based proteomics. However, several major issues exist in the relative isotopic quantification of peptides...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Haskins WE,Petritis K,Zhang J

    更新日期:2011-03-15 00:00:00

  • Unsupervised deep learning reveals prognostically relevant subtypes of glioblastoma.

    abstract:BACKGROUND:One approach to improving the personalized treatment of cancer is to understand the cellular signaling transduction pathways that cause cancer at the level of the individual patient. In this study, we used unsupervised deep learning to learn the hierarchical structure within cancer gene expression data. Deep...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Young JD,Cai C,Lu X

    更新日期:2017-10-03 00:00:00

  • Drug-target interaction prediction using semi-bipartite graph model and deep learning.

    abstract:BACKGROUND:Identifying drug-target interaction is a key element in drug discovery. In silico prediction of drug-target interaction can speed up the process of identifying unknown interactions between drugs and target proteins. In recent studies, handcrafted features, similarity metrics and machine learning methods have...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Eslami Manoochehri H,Nourani M

    更新日期:2020-07-06 00:00:00

  • PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics.

    abstract:BACKGROUND:The number of protein structures from structural genomics centers dramatically increases in the Protein Data Bank (PDB). Many of these structures are functionally unannotated because they have no sequence similarity to proteins of known function. However, it is possible to successfully infer function using o...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: von Grotthuss M,Plewczynski D,Ginalski K,Rychlewski L,Shakhnovich EI

    更新日期:2006-02-06 00:00:00

  • Detecting disease-associated genotype patterns.

    abstract:BACKGROUND:In addition to single-locus (main) effects of disease variants, there is a growing consensus that gene-gene and gene-environment interactions may play important roles in disease etiology. However, for the very large numbers of genetic markers currently in use, it has proven difficult to develop suitable and ...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Long Q,Zhang Q,Ott J

    更新日期:2009-01-30 00:00:00

  • Dynamic changes in the secondary structure of ECE-1 and XCE account for their different substrate specificities.

    abstract:BACKGROUND:X-converting enzyme (XCE) involved in nervous control of respiration, is a member of the M13 family of zinc peptidases, for which no natural substrate has been identified yet. In contrast, it's well characterized homologue endothelin-converting enzyme-1 (ECE-1) showed broad substrate specificity and acts as ...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Ul-Haq Z,Iqbal S,Moin ST

    更新日期:2012-11-01 00:00:00

  • Identifying overrepresented concepts in gene lists from literature: a statistical approach based on Poisson mixture model.

    abstract:BACKGROUND:Large-scale genomic studies often identify large gene lists, for example, the genes sharing the same expression patterns. The interpretation of these gene lists is generally achieved by extracting concepts overrepresented in the gene lists. This analysis often depends on manual annotation of genes based on c...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: He X,Sarma MS,Ling X,Chee B,Zhai C,Schatz B

    更新日期:2010-05-20 00:00:00

  • SpectralNET--an application for spectral graph analysis and visualization.

    abstract:BACKGROUND:Graph theory provides a computational framework for modeling a variety of datasets including those emerging from genomics, proteomics, and chemical genetics. Networks of genes, proteins, small molecules, or other objects of study can be represented as graphs of nodes (vertices) and interactions (edges) that ...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Forman JJ,Clemons PA,Schreiber SL,Haggarty SJ

    更新日期:2005-10-19 00:00:00

  • Stepwise kinetic equilibrium models of quantitative polymerase chain reaction.

    abstract:BACKGROUND:Numerous models for use in interpreting quantitative PCR (qPCR) data are present in recent literature. The most commonly used models assume the amplification in qPCR is exponential and fit an exponential model with a constant rate of increase to a select part of the curve. Kinetic theory may be used to model...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Cobbs G

    更新日期:2012-08-16 00:00:00

  • SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis.

    abstract:BACKGROUND:There are many fewer genes in the human genome than there are expressed transcripts. Alternative splicing is the reason. Alternatively spliced transcripts are often specific to tissue type, developmental stage, environmental condition, or disease state. Accurate analysis of microarray expression data and des...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Kahn AB,Ryan MC,Liu H,Zeeberg BR,Jamison DC,Weinstein JN

    更新日期:2007-03-05 00:00:00

  • Optimal sequencing depth design for whole genome re-sequencing in pigs.

    abstract:BACKGROUND:As whole-genome sequencing is becoming a routine technique, it is important to identify a cost-effective depth of sequencing for such studies. However, the relationship between sequencing depth and biological results from the aspects of whole-genome coverage, variant discovery power and the quality of varian...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Jiang Y,Jiang Y,Wang S,Zhang Q,Ding X

    更新日期:2019-11-08 00:00:00