Predicts magnitude and orientation of the steric component of a molecular alignment tensor. PALES uses the molecule’s three-dimensional (3D) shape to make its prediction. It is not limited to nearly neutral alignment media and can be applied to proteins, nucleic acids and oligosaccharides. The tool can be employed to verify the correctness of derived structures and to evaluate multiple-conformer models for flexible proteins.
Provides a complete software environment for bio nuclear magnetic resonance (NMR) data. NMRbox was developed to simplify discovery and use of NMR software. It also permits users to facilitate software development, deployment, and support. This server also complements BioMagResBank (BMRB), the international data repository for biomolecular NMR data, by simplifying and enriching depositions. It finally provides multiple tools for achieving reproducibility of biomolecular NMR studies.
Builds on orientational principles to allow the efficient interactive calculation and analysis of residual dipolar couplings (RDCs). REDCAT provides a user-friendly program with a graphical-user-interface permitting interaction that can be used for automated data analysis sessions. It includes combined analyses, inclusion of a flexible selection mechanism, imports/exports functions and improvement of the core computational engine.
Allows users to proceed file conversions from 1D nuclear magnetic resonance spectroscopy (NMR) raw formats to nmrML. nmrMLconvert is a software available both as a web application and as a standalone program and includes a comprehensive JAVA-based converter. It accepts Bruker (TOPSPIN, X-WINNMR), Variant/Agilent (VNMRJ) and Jeol (JDF, DELTA) format to be performed from a compiled archive.
Permits to evaluate and compare macromolecular structures. MOLMOL generates high-quality pictures for documentation or publication, such as ribbon presentations and other schematic, simplified views of complex macromolecular structures. It evaluates the torsion angles of the polypeptide backbone. The tool can determine the principal axes of the global molecular shapes and calculates the corresponding radii of gyration.
Provides a suite for trans-omics approaches. ECOMICS is composed of four components: (i) E-class, for taxonomic classification of prokaryotic and eukaryotic DNA sequences, (ii) FT2B to process nuclear magnetic resonance (NMR) spectra for downstream chemical analyses, (iii) Bm-Char which perform an assignment of specific compounds in lignocellulose, and (iv) HetMap to identify and visualize heterogeneous data and correlation matrices.
Allows users to handle multidimensional nuclear magnetic resonance (NMR) data. Nmrglue is a module whose main functions are reading, writing, and interacting with spectral data from multiple commons formats: Bruker, Nmrpipe, Sparky ,Varian/Agilent, Simpson, Rowland. Moreover, the software also includes several common functions for processing the submitted data such as apodization, spectral shifting, or baseline smoothing and flattening. Besides, additional data formats can be implemented.
Allows users to realize proton beam calculations. BGware is a suite of program offering users several types of functions. It includes: (1) BPW; (2) CPO2; (3) FITSCAN; (4) LAMINATE; (5) LOOKUP; (6) NEU; and (7) SCANFOR.
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.