nidhinthomas-ai

AdQuest-Synthetic-Adversarial-Dataset-for-QA-Models

Augmenting the robustness of ELECTRA-Small Question-Answering model using AdQuest, a synthetic adversarial dataset

amberMD

Computational workflow to run MD simulations in AMBER Software.

BBBP_MPNN

Blood-Brain-Barrier Permeability Prediction Using MPNN network

Drug_Discovery_Portal

A collection of web applications to help scientists in computational drug discovery.

ESM-PTM

Prediction of N-Glycosylation Sites in Proteins Using ESM Language Model and Deep Learning

ESM_FineTuning

This repository contains some scripts and Jupyter notebooks exploring how we can fine tune ESM2 protein language model for our custom requirements.

MemProt4MD

A tool to embed transmembrane proteins into lipid membranes using PPM and Packmol

N_Glycan_Epitope_Mapping

This repository describes the workflow for the computational modeling of glycoslylation of protein residues using Rosetta Matcher Protocol.

ViT_ChestXRay_Classification

Fine-tuning of pretrained ViT model for chest X-Ray image classification to detect lung viral infection.

XraySAM

Lung segmentation using fine-tuned model of "Segment Anything" model (SAM) from Meta.

nidhinthomas-ai/AdQuest-Synthetic-Adversarial-Dataset-for-QA-Models

Augmenting the robustness of ELECTRA-Small Question-Answering model using AdQuest, a synthetic adversarial dataset

nidhinthomas-ai/BBBP_MPNN

Blood-Brain-Barrier Permeability Prediction Using MPNN network

nidhinthomas-ai/ESM_FineTuning

This repository contains some scripts and Jupyter notebooks exploring how we can fine tune ESM2 protein language model for our custom requirements.

nidhinthomas-ai/ViT_ChestXRay_Classification

Fine-tuning of pretrained ViT model for chest X-Ray image classification to detect lung viral infection.

nidhinthomas-ai/XraySAM

Lung segmentation using fine-tuned model of "Segment Anything" model (SAM) from Meta.

nidhinthomas-ai/amberMD

Computational workflow to run MD simulations in AMBER Software.

nidhinthomas-ai/Enrichment_Factor

Filtering PROTAC ternary structures to improve Enrichment Factor.

nidhinthomas-ai/ESM-PTM

Prediction of N-Glycosylation Sites in Proteins Using ESM Language Model and Deep Learning

nidhinthomas-ai/MemProt4MD

A tool to embed transmembrane proteins into lipid membranes using PPM and Packmol

nidhinthomas-ai/N_Glycan_Epitope_Mapping

This repository describes the workflow for the computational modeling of glycoslylation of protein residues using Rosetta Matcher Protocol.

nidhinthomas-ai/gmx_MMPBSA

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.

nidhinthomas-ai/GNN_PPI

Codes and models for the paper "Learning Unknown from Correlations: Graph Neural Network for Inter-novel-protein Interaction Prediction".

nidhinthomas-ai/MemProtSim

A workflow to run MD simulations of membrane-protein complex using AMBER.

nidhinthomas-ai/PaperBot

nidhinthomas-ai/pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.

nidhinthomas-ai/PepBot

nidhinthomas-ai/PyAutoFEP

PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods

nidhinthomas-ai/Rosetta_Score_b_factor

This script takes a pdb file generated by Rosetta and extracts the Rosetta Score. Later, adds the rosetta scores to the PDB file as b-factor. The Jupyter notebook describes the code and plots the structure of the protein using Py3Dmol and colors the structure based on b-factor.