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Raviprasad Aduri

Associate Professor

Biophysics of RNA-protein interactions;, Computational Biology
Department of Biological Sciences
BITS Pilani K K Birla Goa campus
NH17B Bypass road
Zuarinagar
Goa 403 726
Raviprasad Aduri

Research Interests

Software Packages Developed by Aduri's lab

xRPI

XRPI is an RNA protein interaction prediction tool developed using extreme gradient boosting (XGBoost) and data driven parameters. The binaries for running the program are provided below. Please follow the instructions provided along with the binaries to run the program. A web server link is also provided. The data sets used in training the ML algorithms are given in the hyperlink below. The external data sets (NPInter v3.0 golden data set and Telopin dataset) used for validating XRPI are also provided.
 
 
 
Citation: 

Jain DS, Gupte SR, Aduri R. “A Data Driven Model for Predicting RNA-Protein Interactions based on Gradient Boosting Machine” Sci. Rep. 8: 9552 (2018; DOI: 10.1038/s41598-018-27814-2)

MP3vec

 

   A Reusable Machine-Constructed Feature Representation for Protein Sequences

 

Multi Purpose Protein Prediction Vector (MP3vec) representation is constructed from a protein’s sequence and its PSSM profile using all the available high resolution protein structural data with the aim to aid in 'transfer learning' to overcome the 'small data' problem in developing predictive models for biomacromolecular interactions. Please refer to the Readme file and the binary can be downloaded as a zip file.

 

Citation: 
 
S. R. Gupte, D. S. Jain, A. Srinivasan and R. Aduri, "MP3vec: A Reusable Machine-Constructed Feature Representation for Protein Sequences," 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Seoul, Korea (South), 2020, pp. 421-425, doi: 10.1109/BIBM49941.2020.9313301.

Molecule Property Predictor

 

With the advancement in Artificial Intelligence, it has been possible to predict things helpful in
chemistry and biology, including drug discovery. Supervised learning has been very fruitful in
predicting the physicochemical properties of small molecules. These models are trained using a
labeled dataset, where the model learns about each data type. The dataset here has 133k stable
small organic molecules with nine heavy atoms (CONF) out of the GDB-17 chemical universe.
A message-passing neural network (MPNN) has been discussed in detail in this paper, along with
novel variations to increase the accuracy of the supervised learning models. The MPNN works
on the idea of the message, update, and readout functions that operate on different graph nodes.
These variations include revamping the input system and adding a semi-master node in the
architecture to increase the overall accuracy to create a robust model. Improvements in the model
will lead to a scalable system for choosing compounds to improve and discover the drugs.
 
 

"Efficient Integration of Molecular Representation and Message-Passing Neural Networks for Predicting Small Molecule Drug-like Properties" by Shreyas Bhat Brahmavar, Mrunmay Mohan Shelar, Revanth Harinarthini, Bandaru Hemantha Sai krishna, Nahush Harihar Kumta, Ojas Wadhwani, Raviprasad Aduri (Manuscript submimtted)

PseMA

Pseudouridine site predictor

Application of ML and DL tools to understand biological systems
 
Predicting RNA protein interactions using domain knowledge (10.1038/s41598-018-27814-2
 
 
Figure 1
 
 
Tools for feature generation and transferable learning for protein sequences (10.1109/BIBM49941.2020.9313301)

 

 

 
 
RNA structure and Dynamics in Viral life cycle (10.1007/s13337-020-00615-w10.1007/s12560-021-09502z)
 
figure1

 
 
 
Annotating RNA Protein Interactions (10.1002/1873-3468.14029)