Prashanth Athri
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View article: Review of Electrostatic Force Calculation Methods and Their Acceleration in Molecular Dynamics Packages Using Graphics Processors
Review of Electrostatic Force Calculation Methods and Their Acceleration in Molecular Dynamics Packages Using Graphics Processors Open
Molecular dynamics (MD) simulations probe the conformational repertoire of macromolecular systems using Newtonian dynamic equations. The time scales of MD simulations allow the exploration of biologically relevant phenomena and can elucida…
Predicting clinical trial outcomes using drug bioactivities through graph database integration and machine learning Open
The ability to estimate the probability of a drug to receive approval in clinical trials provides natural advantages to optimizing pharmaceutical research workflows. Success rates of clinical trials have deep implications to costs, duratio…
Predicting clinical trial outcomes using drug bioactivities through graph database integration and machine learning Open
The ability to estimate the probability of a drug to receive approval in clinical trials provides natural advantages to optimizing pharmaceutical research workflows. Success rates of clinical trials have deep implications to costs, duratio…
Application of Computer-Aided Drug Discovery Methodologies Towards the Rational Design of Drugs Against Infectious Diseases Open
Computer-aided drug discovery involves the application of computer science and programming to solve chemical and biological problems. Specifically, the QSAR (Quantitative Structure Activity Relationships) methodology is used in drug develo…
View article: Predicting Adverse Drug Reactions of Two-drug Combinations using Structural and Transcriptomic Drug Representations to Train a Artificial Neural Network
Predicting Adverse Drug Reactions of Two-drug Combinations using Structural and Transcriptomic Drug Representations to Train a Artificial Neural Network Open
Adverse drug reactions (ADRs) are pharmacological events triggered by drug interactions with various sources of origin including drug-drug interactions. While there are many computational studies that explore models to predict ADRs origina…
View article: Laplacian score and genetic algorithm based automatic feature selection for Markov State Models in adaptive sampling based molecular dynamics
Laplacian score and genetic algorithm based automatic feature selection for Markov State Models in adaptive sampling based molecular dynamics Open
Adaptive sampling molecular dynamics based on Markov State Models use short parallel MD simulations to accelerate simulations, and are proven to identify hidden conformers. The accuracy of the predictions provided by it depends on the feat…
2ORP-ligand_Babel.pdb Open
PDB Altered by Babel
PROTEINATOR: Web-UI exploring repurposing hypotheses of PROTEIN InhibiTORs based on protein interactions Open
PROTEINATOR is the first version of a staggered, multi-paradigm and extensible drug repurposing platform, focusing on a novel data analytic and integration strategy to find repurposing candidates that have potential to modulate targets thr…
Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources Open
In recent years, the emphasis of scientific inquiry has shifted from whole-genome analyses to an understanding of cellular responses specific to tissue, developmental stage or environmental conditions. One of the central mechanisms underly…
Web-based drug repurposing tools: a survey Open
Drug repurposing (a.k.a. drug repositioning) is the search for new indications or molecular targets distinct from a drug's putative activity, pharmacological effect or binding specificities. With the ever-increasing rates of termination of…
Genetic‐Algorithm‐Based Optimization of a Peptidic Scaffold for Sequestration and Hydration of CO<sub>2</sub> Open
Biomimicry is a strategy that makes practical use of evolution to find efficient and sustainable ways to produce chemical compounds or engineer products. Exploring the natural machinery of enzymes for the production of desired compounds is…