SergeiNikolenko

AntibodyCluster

The AntibodyCluster repository contains scripts designed to extract sequences of amino acid chains from antibodies present in Protein Data Bank (PDB) format files. The scripts employ the SAbDab database for file processing.

ChemRar

The project aims to build and evaluate machine learning models for predicting the biological activity of molecules. Both graph neural networks (GCN, GAT, GIN) and the XGBoost model based on molecular fingerprints (ECFP4) are used.

DeepMD_crystal_generator

This repository provides a toolkit for modeling co-crystals. It includes efficient scripts for DeepMD and ACE, optimized for cluster execution with slurm and screen.

ERa

fukui_index_prediction

This project develops a machine learning model using Chebyshev graph convolutions within a Kernel-based Attention Network (KAN) to accurately predict Fukui indices, which are essential for assessing molecular reactivity in chemical reactions.

ImmunoPeptideDesigner

Automated generation of immunogenic peptides from protein structures and molecular docking analysis using AlphaFold2 and AutodockVina.

ksitest

The goal is to impute STR (Short Tandem Repeats) data from SNP (Single Nucleotide Polymorphisms) data for Holstein cows, which is critical in verifying the genetic relationship between animals for livestock selection.

leash-BELKA

LPCE

The LPCE project is designed to purify and process PDB structures to extract and filter ligands and remove unwanted components such as water molecules and junk ligands.

py4chemoinformatics

Python for chemoinformatics

SergeiNikolenko/DeepMD_crystal_generator

This repository provides a toolkit for modeling co-crystals. It includes efficient scripts for DeepMD and ACE, optimized for cluster execution with slurm and screen.

SergeiNikolenko/AntibodyCluster

The AntibodyCluster repository contains scripts designed to extract sequences of amino acid chains from antibodies present in Protein Data Bank (PDB) format files. The scripts employ the SAbDab database for file processing.

SergeiNikolenko/ERa

SergeiNikolenko/ImmunoPeptideDesigner

Automated generation of immunogenic peptides from protein structures and molecular docking analysis using AlphaFold2 and AutodockVina.

SergeiNikolenko/leash-BELKA

SergeiNikolenko/py4chemoinformatics

Python for chemoinformatics

SergeiNikolenko/AutoGPT

AutoGPT is the vision of accessible AI for everyone, to use and to build on. Our mission is to provide the tools, so that you can focus on what matters.

SergeiNikolenko/BIOCAD-winter-internship

SergeiNikolenko/chem_tutorial

SergeiNikolenko/ChemRar

The project aims to build and evaluate machine learning models for predicting the biological activity of molecules. Both graph neural networks (GCN, GAT, GIN) and the XGBoost model based on molecular fingerprints (ECFP4) are used.

SergeiNikolenko/fukui_index_prediction

This project develops a machine learning model using Chebyshev graph convolutions within a Kernel-based Attention Network (KAN) to accurately predict Fukui indices, which are essential for assessing molecular reactivity in chemical reactions.

SergeiNikolenko/geropharm-test_case

SergeiNikolenko/ksitest

The goal is to impute STR (Short Tandem Repeats) data from SNP (Single Nucleotide Polymorphisms) data for Holstein cows, which is critical in verifying the genetic relationship between animals for livestock selection.

SergeiNikolenko/LPCE

The LPCE project is designed to purify and process PDB structures to extract and filter ligands and remove unwanted components such as water molecules and junk ligands.

SergeiNikolenko/practical_cheminformatics_tutorials

Practical Cheminformatics Tutorials

SergeiNikolenko/SergeiNikolenko

Hi! This is my start page with my resume, good to see you!

SergeiNikolenko/useful_rdkit_utils

Some useful RDKit functions

SergeiNikolenko/chemprop

Message Passing Neural Networks for Molecule Property Prediction

SergeiNikolenko/cookiecutter-data-science

A logical, reasonably standardized, but flexible project structure for doing and sharing data science work.

SergeiNikolenko/deepchem

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

SergeiNikolenko/descriptastorus

Descriptor computation(chemistry) and (optional) storage for machine learning

SergeiNikolenko/gat

SergeiNikolenko/Meeko

Interfacing RDKit and AutoDock

SergeiNikolenko/orca

SergeiNikolenko/QM_descriptors_calculation

SergeiNikolenko/QuantumChemistryGang

This repository is dedicated to the storage and documentation of computational assignments and projects related to the Quantum Chemistry course. It contains theoretical calculations, computational models, and analysis reports for various molecules.

SergeiNikolenko/reactivity_predictions_substitution

Platforms to predict reactivity for substitution reactions.

SergeiNikolenko/single_cell_perturbations

3rd place solution in Open Problems – Single-Cell Perturbations. This is a regression problem of 2 feature columns and 18211 targets.

SergeiNikolenko/tg2obsidian

This script pulls new messages from a Telegram group and puts them into Obsidian vault on a local machine