A program for analyzing the binding affinity of amyloid proteins. SEMBA uses an energy function that computes the Lennard-Jones, Coulomb, and solvation energies to determine the effect of a mutation on a protein's stability.
Allows users to select density functional and basis set combinations. The Decider is a web application that is based on game theory coupled with existing benchmark data. It is composed of two mains panels that permits either to draw molecules that have to be evaluated and a to list panel that compiles the results and their scores. The platform aims to assists chemists in performing density functional theory calculations.
A web server for predicting and designing of quorum sensing peptides. QSPpred web server hosts SVM based predictive models i.e. QSPepPred, QSPepDesign and QSPepMap utilizing compositional, binary, physicochemical features and their hybrids. QSPepPred predicts the extent of an input peptide (fasta or multifasta format) as QSP or non-QSP. QSPepDesign can design all possible single position mutants of a given peptide sequence and subsequently predict their QS status. QSPepMap helps to identify potential regions in protein, which may function as QSPs. In addition, it also includes various analysis tools like QSMotifScan, MutGen, PhysicoProp and ProtFrag.
Serves as a one-stop analysis and visualization tool for bioactive peptide discovery. SpirPep can predict putative peptides via the in-silico digestion of protein up to a genome-wide level. This software exploits 13 databases of antimicrobial, anticancer and antibacterial peptides and other bioactive peptides. It features genome-wide scale inputs, a miscleavage option, the output of a number of known bioactive peptides for bioactivity identifier, the resulting peptide categorized by enzyme and an original protein tracker.
Enables construction of profiles of the potential biological activity of protein fragments. BIOPEP includes a database of biologically active peptide sequences including proteolytic processes design. This software counts quantitative descriptors as measures of the value of proteins as possible precursors of bioactive peptides. I can predict bonds susceptible to hydrolysis by endopeptidases in a protein chain.
Dr. Yashwanth Subbannayya obtained his M.Sc. degree in Medical Biochemistry from Manipal University. He qualified the competitive CSIR-UGC National Eligibility Test and joined the Institute of Bioinformatics, Bangalore as a UGC Junior Research Fellow. As part of his Ph.D. work, he studied the molecular mechanisms of gastric cancer in clinical specimens using quantitative proteomic technologies. This study, the results of which were published in Cancer Biology and Therapy, yielded a novel therapeutic target for gastric cancer- CAMKK2. Further, he also studied the serum proteome of gastric cancer patients and developed assays for potential markers using the revolutionary multiple reaction monitoring approach. The results of this study were published in Journal of Proteomics. In addition to his research work, he also trained extensively in sample preparation for mass spectrometry, fractionation techniques and gained expertise in quantitative proteomic techniques and data analysis. In addition, he also trained extensively in various validation platforms including immunohistochemsitry, multiple reaction monitoring and Western blot. He has also worked as a curator for several biological databases including NetPath, Human Protein Reference Database (HPRD) and Breast cancer database. His work in various research projects have yielded him 23 publications either as lead author or co-author in peer reviewed journals. He is a reviewer for the journal Proteomics.
Dr. Yashwanth Subbannayya joined the YU-IOB Center for Systems Biology and Molecular Medicine in June, 2015. During the initial period, his job consisted of assisting other personnel of the university in the establishment of YU-IOB Center for Systems Biology and Molecular Medicine. He was also involved in training of Ph.D. students in biological aspects. After the establishment of the center, he trained in cell culture techniques and metabolomics analysis. At YU-IOB CSBMM, he is studying the molecular mechanisms in various cancers including oral cancer. In addition, he is studying the molecular mechanisms as well as the metabolic constituents of traditional medicine formulations using mass spectrometry technologies. In June 2016, he convened the national symposium “Genomics in clinical practice: Future of precision medicine” held at Yenepoya University on June 1 and 2, 2016. The resource persons included 16 individuals from various academic organizations as well as industry. The symposium was attended by 218 participants from 24 institutions around India. He is a member of the Scientific Review Board of Yenepoya Research Centre where he facilitates timely scientific review of research projects.