Biomedical Informatics Center

Lal Bahadur Nagar, India

Biomedical Informatics Center

Lal Bahadur Nagar, India
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Malik A.,Biomedical Informatics Center | Firoz A.,Biomedical Informatics Center | Jha V.,Biomedical Informatics Center | Sunderasan E.,Biotechnology Unit | Ahmad S.,Japan National Institute of Biomedical Innovation
Journal of Molecular Modeling | Year: 2010

Rubber trees infected with a host-specific cassiicolin toxin often experience considerable leaf fall, which in turn results in loss of crop productivity. It was recently revealed that cassiicolin-specific single-chain variable fragments (scFv) can successfully reduce the toxic effects of cassiicolin. However, the detailed mechanism of antibody action remains poorly understood. The primary sequence of the newly sequenced cassiicolin-specific scFv was highly homologous to several members of single-chain antibodies in the 14B7 family. In this study, with the aid of homology modeling, the three-dimensional structure of cassiicolinspecific scFv was elucidated, and was found to exhibit a characteristic immunoglobulin fold that mainly consists of β sheets Additionally, molecular docking between the modeled scFv antibody and the available three-dimensional crystal structure of cassiicolin toxin was also performed' The predicted structural complex and the change in accessible surface area between the toxin and the scFv antibody upon complexation reveal the potential role of certain complementarity determining region (CDR) amino acid residues in the formation of the complex These computational results suggest that mutagenesis experiments that are aimed at validating the model and improving the binding affinity of cassiicolin-specific scFv antibodies for the toxin should be performed. © Springer-Verlag 2010.

Sundaramurthi J.C.,Biomedical Informatics Center | Brindha S.,University of Madras | Reddy T.B.K.,Stanford University | Hanna L.E.,Biomedical Informatics Center
Tuberculosis | Year: 2012

Integration of biological data on gene sequence, genome annotation, gene expression, metabolic pathways, protein structure, drug target prioritization and selection, has resulted in several online bioinformatics databases and tools for Mycobacterium tuberculosis. Alongside there has been a growth in the list of cheminformatics databases for small molecules and tools to facilitate drug discovery. In spite of these efforts there is a noticeable lag in the drug discovery process which is an urgent need in the case of emerging and re-emerging infectious diseases. For example, more than 25 online databases are available freely for tuberculosis and yet these resources have not been exploited optimally. Informatics-centered drug discovery based on the integration and analysis of both bioinformatics and cheminformatics data could fill in the gap and help to accelerate the process of drug discovery. This article aims to review the current standing of developments in tuberculosis-bioinformatics and highlight areas where integration of existing resources could lead to acceleration of drug discovery against tuberculosis. Such an approach could be adapted for other diseases as well. © 2011 Elsevier Ltd. All rights reserved.

PubMed | Yogi Vemana University and Biomedical Informatics Center
Type: | Journal: Gene | Year: 2016

In-silico attempt was made to identify the key hub genes which get differentially expressed in biliary stricture and hepatic carcinoma. Gene expression data, GSE34166, was downloaded from the GEO database, which contains 10 biliary stricture samples (4 benign control and 6 malignant carcinoma), for screening of key hub genes associated with the disease. R packages scripts were identified 85 differentially expressed genes. Further these genes were uploaded in WebGestalt database and identified nine key genes. Using STRING database and Gephi software, the protein-protein interaction networks were constructed and also studied gene ontology through WebGestalt. Finally, we identified four key genes (CXCR4, ADH1C, ABCB1 and ADH1A) are associated with liver carcinoma and further cross-validated with Liverome, Protein Atlas database and bibliography. In addition, transcription factors and their binding sites also studied. These identified hub genes and their transcription factors are the probable potential targets for possible future drug design.

Kumar M.,Tuberculosis Research Center | Meenakshi N.,Government Thiruvotteeswarar Hospital of Thoracic Medicine | Sundaramurthi J.C.,Biomedical Informatics Center | Kaur G.,All India Institute of Medical Sciences | And 2 more authors.
Tuberculosis | Year: 2010

The 6-kDa early secreted antigenic target (ESAT-6) is a T-cell antigen recognized by individuals infected with Mycobacterium tuberculosis. The aim of the study was to identify "protective epitopes" of ESAT-6 protein in the south Indian population. Proliferative and Interferon gamma (IFN-γ) responses to ESAT-6 peptides were studied by flow cytometry and Enzyme linked immunosorbent assay (ELISA). Healthy household contacts (HHC) recognized Esp1 (10/17) and Esp6 (9/17) peptides. Among pulmonary tuberculosis patients (PTB), Esp1 (3/11) and Esp6 (5/11) were recognized. Maximal response (7/10) was found for Esp1 and Esp8 in treated patients (TR). Median values for the responding subjects gave the following results: Esp1 (76 pg/ml), Esp6 (64 pg/ml), induced IFN-γ production in HHC; PTB gave low IFN-γ responses for the peptides. TR responded to the peptides Esp1 (141 pg/ml), Esp8 (102 pg/ml). The proliferation of CD4 cells was similar in both PTB and TR for all peptides; but HHC showed an increase for Esp1 (p < 0.05) and Esp6 (p < 0.01). Esp1 (amino acids aa 1-20) and Esp6 (aa 51-70) were the immunogenic peptides recognized by the alleles HLA DRB1*04 and HLA DRB1*10 among HHC. But the association of the alleles with ESAT-6 peptide presentation needs to be confirmed in a large cohort of subjects. We speculate that ESAT-6 can be used along with other immune-eliciting proteins for vaccine design strategies in south Indian population. © 2009 Elsevier Ltd. All rights reserved.

Yellapu N.K.,Biomedical Informatics Center | Pulaganti M.,Multi Disciplinary Research Unit | Pakala S.B.,Indian Institute of Science
Journal of Biomolecular Structure and Dynamics | Year: 2016

P21-activated kinase-1 (PAK1) is an enzyme associated with multiple metabolic networks and different types of cancers. Hence, there is a need to study the global network map of PAK1 to understand its role and regulatory mechanisms by means of its significant molecular interactive partners. This will help to explore its global biological functions in breast cancer. In view of this, we obtained the gene expression data-sets of PAK1 from The Cancer Genome Atlas-cBioportal and GeneCards databases and found that 91 PAK1-related genes are associated with breast cancer. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway investigations of 91 genes via Database for Annotation Visualization and Integrated Discovery bioinformatics resource revealed that, PAK1 being a major kinase is associated with several metabolic pathways and involved in phosphorylation, signal transduction, apoptosis, biosynthesis and majorly cancer-related cell signalling pathways. The PAK1 interaction network derived from STRING and Cytoscape revealed that the genes Signal-Transducer-and-Activator-of-Transcription-3 (STAT3), Cyclin-D1 (CCND1), Mitogen-activated protein kinase-1 (MAPK1), Ras-Homolog-Family-Member-A (RHOA) and Catenin-beta-1 have high degrees of interaction where CCND1, MAPK1 and RHOA have direct interaction with PAK1. Finally, the global expression map of PAK1 and its related genes was derived as topological frame that helped to explore and investigate PAK1 interactions. Further, the molecular modelling studies of PAK1 with its major interacting partners RHOA and STAT3 helped to explore the key interactive residues of PAK1 structure. This information can be used to develop novel therapeutic and control strategies against breast cancer. © 2016 Informa UK Limited, trading as Taylor & Francis Group

Firoz A.,Biomedical Informatics Center | Malik A.,Biomedical Informatics Center | Joplin K.H.,East Tennessee State University | Ahmad Z.,Alabama A&M University | And 2 more authors.
BMC Biochemistry | Year: 2011

Background: Adenine and guanine phosphates are involved in a number of biological processes such as cell signaling, metabolism and enzymatic cofactor functions. Binding sites in proteins for these ligands are often detected by looking for a previously known motif by alignment based search. This is likely to miss those where a similar binding site has not been previously characterized and when the binding sites do not follow the rule described by predefined motif. Also, it is intriguing how proteins select between adenine and guanine derivative with high specificity. Results: Residue preferences for AMP, GMP, ADP, GDP, ATP and GTP have been investigated in details with additional comparison with cyclic variants cAMP and cGMP. We also attempt to predict residues interacting with these nucleotides using information derived from local sequence and evolutionary profiles. Results indicate that subtle differences exist between single residue preferences for specific nucleotides and taking neighbor environment and evolutionary context into account, successful models of their binding site prediction can be developed. Conclusion: In this work, we explore how single amino acid propensities for these nucleotides play a role in the affinity and specificity of this set of nucleotides. This is expected to be helpful in identifying novel binding sites for adenine and guanine phosphates, especially when a known binding motif is not detectable. © 2011 Firoz et al; licensee BioMed Central Ltd.

Kumar M.,Tuberculosis Research Center | Sundaramurthi J.C.,Biomedical Informatics Center | Mehra N.K.,All India Institute of Medical Sciences | Kaur G.,All India Institute of Medical Sciences | Raja A.,Tuberculosis Research Center
Medical Microbiology and Immunology | Year: 2010

The Mycobacterium tuberculosis (M. tuberculosis)-specific culture filtrate protein-10 (CFP-10) is highly recognized by M. tuberculosis infected subjects. In the present study, the proliferative response and IFN-γ secretion was found for C-terminal peptides of the protein (Cfp651-70, Cfp7 61-80, Cfp871-90, and Cfp981-100). The alleles HLA DRB104 and HLA DRB110 recognized the C-terminal peptides Cfp7, Cfp8, and Cfp9 in HHC. Cfp6 was predominantly recognized by the alleles HLA DRB103 and HLA DRB115 by PTB. The minimal nonameric epitopes from the C-terminal region were CFP-1056-64 and CFP-1076-84. These two peptides deserve attention for inclusion in a vaccine against tuberculosis in this region. © 2009 Springer-Verlag.

Nanda Kumar Y.,Biomedical Informatics Center | Jeyakodi G.,Biomedical Informatics Center | Gunasekaran K.,Biomedical Informatics Center | Jambulingam P.,Biomedical Informatics Center
Journal of Biomolecular Structure and Dynamics | Year: 2016

Plasmodium vivax is the most prevalent species of malaria affecting millions of people annually worldwide and demands effective interventions to develop a successful vaccine. In this milieu, we have dedicated noteworthy efforts to characterize the proteome of P. vivax to give a lead for the epitope-based vaccine development. Membrane proteins of P. vivax were collected from SWISS PROT database and 10 antigenic proteins were identified among them by in silico analysis using multiple servers. T-cell and B-cell epitopes were identified and their immunity was assessed. Their ability to trigger humoral and cell-mediated responses was determined. Three dimensional models were constructed for the antigenic proteins using Modeller, Phyre2, and Modloop tools and their quality was validated using PROCHECK and ProSA-web validation servers. Further, the binding affinity and molecular interactions of these antigenic proteins were characterized by performing protein–protein docking against transmission-blocking anti-malaria antibody Fab2A8 (PDB ID: 3S62) using Z-dock module of Discovery Studio 4.0. The presence of potential B & T-cell epitopes, major histocompatibility complex-binding sites, and their efficient interactions with Fab2A8 antibody suggests the use of predicted antigenic proteins for the construction of multi-epitope peptide vaccine against P. vivax. © 2015 Informa UK Limited, trading as Taylor & Francis Group.

PubMed | Biomedical Informatics Center
Type: | Journal: Journal of molecular graphics & modelling | Year: 2016

The protein kinases (PKs), belonging to serine/threonine kinase (STKs), are important drug targets for a wide spectrum of diseases in human. Among protein kinases, the Casein Kinases (CKs) are vastly expanded in various organisms, where, the malarial parasite Plasmodium falciparum possesses a single member i.e., PfCKI, which can phosphorylate various proteins in parasite extracts in vitro condition. But, the structure-function relationship of PfCKI and dynamics of ATP binding is yet to be understood. Henceforth, an attempt was made to study the dynamics, stability, and ATP binding mechanisms of PfCKI through computational modelling, docking, molecular dynamics (MD) simulations, and MM/PBSA binding free energy estimation. Bi-lobed catalytic domain of PfCKI shares a high degree of secondary structure topology with CKI domains of rice, human, and mouse indicating co-evolution of these kinases. Molecular docking study revealed that ATP binds to the active site where the glycine-rich ATP-binding motif (G16-X-G18-X-X-G21) along with few conserved residues plays a crucial role maintaining stability of the complex. Structural superposition of PfCKI with close structural homologs depicted that the location and length of important loops are different, indicating the dynamic properties of these loops among CKIs, which is consistent with principal component analysis (PCA). PCA displayed that the overall global motion of ATP-bound form is comparatively higher than that of apo form. The present study provides insights into the structural features of PfCKI, which could contribute towards further understanding of related protein structures, dynamics of catalysis and phosphorylation mechanism in these important STKs from malarial parasite in near future.

PubMed | Regional Medical Research Center and Biomedical Informatics Center
Type: Journal Article | Journal: Glycoconjugate journal | Year: 2015

Mucins are major glycoprotein components of the mucus that coats the surfaces of cells lining the respiratory, digestive, gastrointestinal and urogenital tracts. They function to protect epithelial cells from infection, dehydration and physical or chemical injury, as well as to aid the passage of materials through a tract i.e., lubrication. They are also implicated in the pathogenesis of benign and malignant diseases of secretory epithelial cells. In Human there are two types of mucins, membrane-bound and secreted that are originated from mucous producing goblet cells localized in the epithelial cell layer or in mucous producing glands and encoded by MUC gene. Mucins belong to a heterogeneous family of high molecular weight proteins composed of a long peptidic chain with a large number of tandem repeats that form the so-called mucin domain. The molecular weight is generally high, ranging between 0.2 and 10 million Dalton and all mucins contain one or more domains which are highly glycosylated. The size and number of repeats vary between mucins and the genetic polymorphism represents number of repeats (VNTR polymorphisms), which means the size of individual mucins can differ substantially between individuals which can be used as markers. In human it is only MUC1 and MUC7 that have mucin domains with less than 40% serine and threonine which in turn could reduce number of PTS domains. Mucins can be considered as powerful two-edged sword, as its normal function protects from unwanted substances and organisms at an arms length while, malfunction of mucus may be an important factor in human diseases. In this review we have unearthed the current status of different mucin proteins in understanding its role and function in various non-communicable diseases in human with special reference to its organ specific locations. The findings described in this review may be of direct relevance to the major research area in biomedicine with reference to mucin and mucin associated diseases.

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