Performs molecular dynamics simulations and energy minimization. GROMACS provides a rich set of calculation types, preparation and analysis tools. It also distributes computational work across ensembles of simulations, multiple program paths and domains within simulations, multiple cores working on each domain, exploiting instruction-level parallelism across those cores handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in.
Provides an approach for the generation of ligand images filling protein pockets based on deep neural networks. LigVoxel produces predictions that are responsive to the number of atoms selected as input. These predictions significantly overlap with ligand features of previously unseen ligands, and they can be used to select poses and conformers close to the native ligand orientation and geometry.
A molecular dynamics and modeling framework for the determination of the structure and dynamics of proteins and nucleic acids. Almost aims to provide support for a wide range of different structure determination protocols that make use of experimental observables as conformational restraints. To achieve its objectives, Almost has been designed with a flexible architecture, consisting of three application layers : (i) core data structures for the computational representation of molecules, (ii) core algorithms required for an efficient calculation of energies and interaction forces, (iii) methods and algorithms for the structural analysis and assessment of structures and trajectories.
Allows simulations of arbitrary mixtures of both rigid and flexible molecules. MDynaMix is a general purpose molecular dynamics simulation package that employs a double time step algorithm for fast and slow modes, an Ewald method for electrostatic interactions, and a constant temperature constant-pressure algorithm. The software was used in simulations of very different molecular systems.
Allows molecular simulation. CHARMM is a program that focuses on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. The software offers a set of energy functions and several sampling methods. It has applications for many-particle systems, as well as for inorganic materials, with applications in materials design.
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.
emmanuel Ph.D. student in Structural Bioinformatics
University of Bergen