ramirezlab/ramirezlab.github.io

The Website of the Ramiréz Lab

Language: HTML - Size: 297 MB - Last synced: about 2 hours ago - Pushed: about 3 hours ago - Stars: 2 - Forks: 1

DrugBud-Suite/DockM8

All in one Structure-Based Vitual Screening workflow based on the concept of consensus docking.

Language: Jupyter Notebook - Size: 179 MB - Last synced: about 3 hours ago - Pushed: about 9 hours ago - Stars: 7 - Forks: 0

tagirshin/altmol

Plugin to show molecule images on mouseover using RDKit and Altair

Language: Jupyter Notebook - Size: 4.49 MB - Last synced: about 6 hours ago - Pushed: 1 day ago - Stars: 4 - Forks: 1

experimental-design/bofire

Experimental design and (multi-objective) bayesian optimization.

Language: Jupyter Notebook - Size: 27.4 MB - Last synced: about 8 hours ago - Pushed: about 12 hours ago - Stars: 106 - Forks: 20

BTSpeake/ChemToolKit

A computational chemistry tool kit including file handling and molecular manipulation tools.

Language: C++ - Size: 207 KB - Last synced: about 8 hours ago - Pushed: about 9 hours ago - Stars: 0 - Forks: 0

ThomasCsson/MASSIVEChem

MASSIVEChem is a pip-installable package centred around mass spectrometry

Language: Python - Size: 1.67 MB - Last synced: about 10 hours ago - Pushed: about 10 hours ago - Stars: 2 - Forks: 0

protwis/gpcrdb_data

This repository is the collection point of reference data for the GPCRdb. The GPCRdb contains reference data, interactive visualisation and experiment design tools for G protein-coupled receptors (GPCRs).

Language: HTML - Size: 979 MB - Last synced: about 14 hours ago - Pushed: about 15 hours ago - Stars: 24 - Forks: 28

rdkit/rdkit

The official sources for the RDKit library

Language: HTML - Size: 195 MB - Last synced: about 15 hours ago - Pushed: about 16 hours ago - Stars: 2,446 - Forks: 841

gnina/gnina

A deep learning framework for molecular docking

Language: C++ - Size: 240 MB - Last synced: about 17 hours ago - Pushed: 1 day ago - Stars: 556 - Forks: 140

reskyner/BruteReg

Language: Python - Size: 95.5 MB - Last synced: about 18 hours ago - Pushed: over 6 years ago - Stars: 1 - Forks: 1

chembl/chembl_webresource_client

Official Python client for accessing ChEMBL API

Language: Python - Size: 2.17 MB - Last synced: about 17 hours ago - Pushed: 3 months ago - Stars: 353 - Forks: 94

JelfsMaterialsGroup/stko

A collection of molecular optimisers and property calculators for use with stk.

Language: Python - Size: 1.94 MB - Last synced: about 1 month ago - Pushed: 3 months ago - Stars: 19 - Forks: 7

JoseRodriguezRomero/MolFFSim

A C++ implementation of an OFDFT based molecular force field model.

Language: C++ - Size: 193 KB - Last synced: about 8 hours ago - Pushed: 1 day ago - Stars: 1 - Forks: 0

Smoren/molecular-ts

Virtual chemistry simultaion. Visualization of the behavior of particles in two-dimensional and three-dimensional space.

Language: TypeScript - Size: 29 MB - Last synced: about 21 hours ago - Pushed: 1 day ago - Stars: 16 - Forks: 0

matteoferla/Fragmenstein

Merging, linking and placing compounds by stitching bound compounds together like a reanimated corpse

Language: Python - Size: 15.6 MB - Last synced: about 4 hours ago - Pushed: 1 day ago - Stars: 160 - Forks: 13

pckroon/pysmiles

A lightweight python-only library for reading and writing SMILES strings

Language: Python - Size: 161 KB - Last synced: about 24 hours ago - Pushed: 1 day ago - Stars: 132 - Forks: 20

rudolphi/open_enventory

PHP/MySQL-based chemical inventory/Electronic Lab Notebook for chemistry

Language: PHP - Size: 28.9 MB - Last synced: about 20 hours ago - Pushed: 1 day ago - Stars: 10 - Forks: 6

openbabel/openbabel

Open Babel is a chemical toolbox designed to speak the many languages of chemical data.

Language: C++ - Size: 72.5 MB - Last synced: about 23 hours ago - Pushed: 9 days ago - Stars: 1,001 - Forks: 405

matteoferla/Fragment-hit-follow-up-chemistry

A collection of notebooks and scripts for the prediction of follow-up compounds in

Language: Jupyter Notebook - Size: 3.41 MB - Last synced: about 22 hours ago - Pushed: 1 day ago - Stars: 9 - Forks: 0

ale94mleon/MolDrug

MolDrug is a python package for drug-oriented optimization on the chemical space ​

Language: Python - Size: 98.8 MB - Last synced: about 23 hours ago - Pushed: 1 day ago - Stars: 10 - Forks: 2

JensKrumsieck/ChemSharp

Library for processing of chemistry related files (aiming at spectroscopy and structural files)

Language: C# - Size: 6.7 MB - Last synced: 1 day ago - Pushed: 3 months ago - Stars: 11 - Forks: 5

BrightBlueCheese/transformers_and_chemistry

The Role of Model Architecture and Scale in Predicting Molecular Properties: Insights from Fine-Tuning RoBERTa, BART, and LLaMA

Language: Jupyter Notebook - Size: 414 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 0 - Forks: 0

tlint101/py50

Generate Dose-Response Curves in Python

Language: Jupyter Notebook - Size: 9.9 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 4 - Forks: 2

NoeDemange/Cage-Moleculaire

Génération de guides de cages moléculaires

Language: C - Size: 6.95 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 0 - Forks: 0

fazekaszs/loco_hd

The LoCoHD metric for protein-protein structure comparison

Language: Python - Size: 2.68 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 0 - Forks: 0

Henrium/MolSets

Molecular graph deep sets learning for mixture property modeling.

Language: Python - Size: 499 KB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 5 - Forks: 0

mpecchi/hplc_data_analysis

Automating HPLC data analysis in Python

Language: Python - Size: 825 KB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 2 - Forks: 0

rflameiro/Python_e_Quiminformatica

Tutoriais sobre Python, Aprendizado de Máquina e Quiminformática (em português)

Language: Jupyter Notebook - Size: 10.2 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 0 - Forks: 0

ksharindam/chemcanvas

A very intuitive 2D chemical drawing tool

Language: Python - Size: 519 KB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 5 - Forks: 0

pierrehirel/atomsk

Atomsk: A Tool For Manipulating And Converting Atomic Data Files -

Language: Fortran - Size: 4 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 183 - Forks: 73

kuulia/BESPE-MACCS

A proof-of-concept type demo of the Binary Encoded SMARTS Pattern Enumeration + Molecular aCCess System molecular descriptor developed as part of Bachelor's Thesis: "Feature engineering for machine learning predictions in atmospheric science." Includes a toy data set for demonstrative purposes.

Language: Python - Size: 1.76 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 0 - Forks: 0

ideaconsult/pynanomapper

A Python client for the eNanoMapper API

Language: Python - Size: 375 KB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 0 - Forks: 1

cdk/cdk

The Chemistry Development Kit

Language: Java - Size: 236 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 469 - Forks: 153

egonw/bacting

Bacting is an open-source platform for chemo- and bioinformatics based on Bioclipse that defines a number of common domain objects and wraps common functionality, providing a toolkit independent, scriptable solution to handle data from the life sciences.

Language: Java - Size: 1.26 MB - Last synced: about 13 hours ago - Pushed: about 14 hours ago - Stars: 12 - Forks: 5

Sulstice/Uptime-Cheminformatics

📈 Uptime monitor and status page for Suliman Sharif, powered by @upptime

Language: Markdown - Size: 3.04 GB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 11 - Forks: 3

asarigun/awesome-denovo-papers

Awesome De novo drugs design papers

Size: 57.6 KB - Last synced: 4 days ago - Pushed: 6 months ago - Stars: 75 - Forks: 10

jvalegre/aqme

Automated Quantum Mechanical Environments (AQME) offers transparent and reproducible workflows available for Jupyter Notebooks and command lines, including: 1) RDKit- and CREST-based conformer generation, 2) QM input file creation, 3) post-processing of QM output files, 4) generation of xTB, DFT and RDKit descriptors. https://aqme.readthedocs.io

Language: Python - Size: 81.6 MB - Last synced: 5 days ago - Pushed: 6 days ago - Stars: 88 - Forks: 21

partridgejiang/Kekule.js

A Javascript cheminformatics toolkit.

Language: JavaScript - Size: 111 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 244 - Forks: 60

egonw/cdk Fork of cdk/cdk

The Chemistry Development Kit

Language: Java - Size: 161 MB - Last synced: 5 days ago - Pushed: 6 days ago - Stars: 1 - Forks: 1

mqcomplab/iSIM

Module containing scripts to perform multiple comparison simultaneously and getting the exact same value as the average pairwise comparisons of molecules represented by binary fingerprints or real number descriptors.

Language: Jupyter Notebook - Size: 602 KB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 14 - Forks: 6

nanxstats/Rcpi

💊 Molecular informatics toolkit with integration of bioinformatics and cheminformatics tools for drug discovery

Language: R - Size: 10.3 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 35 - Forks: 12

datamol-io/datamol

Molecular Processing Made Easy.

Language: Python - Size: 111 MB - Last synced: 11 days ago - Pushed: 3 months ago - Stars: 426 - Forks: 46

virtualramblas/awesome-deep-learning-4-life-sciences

A collection of resources for Deep Learning in Python for Life Sciences (with focus on biotech and pharma).

Size: 1.93 MB - Last synced: about 9 hours ago - Pushed: 2 months ago - Stars: 87 - Forks: 10

Global-Chem/global-chem

A Knowledge Graph of Common Chemical Names to their Molecular Definition

Language: Jupyter Notebook - Size: 114 MB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 141 - Forks: 19

lightaime/deep_gcns_torch

Pytorch Repo for DeepGCNs (ICCV'2019 Oral, TPAMI'2021), DeeperGCN (arXiv'2020) and GNN1000(ICML'2021): https://www.deepgcns.org

Language: Python - Size: 7.02 MB - Last synced: 3 days ago - Pushed: almost 2 years ago - Stars: 1,119 - Forks: 156

vtarasv/pocket-cfdm

Augmenting a training dataset of the generative diffusion model for molecular docking with artificial binding pockets

Language: Python - Size: 26.4 KB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 9 - Forks: 1

sirius-ms/sirius

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)

Language: Java - Size: 44.2 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 75 - Forks: 17

Meredith-Lab/volcalc

volcalc: Calculate Volatility of Chemical Compounds

Language: R - Size: 4.6 MB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 4 - Forks: 1

egonw/cdkbook

Groovy Cheminformatics with the Chemistry Development Kit

Language: Groovy - Size: 11.3 MB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 39 - Forks: 11

chemplusx/ChemInstruct

Chemical Named Entity Recognition Training and Testing Tool

Language: Python - Size: 163 MB - Last synced: 6 days ago - Pushed: 9 days ago - Stars: 0 - Forks: 1

egonw/chempyformatics

Language: Groovy - Size: 37.1 KB - Last synced: 7 days ago - Pushed: 8 days ago - Stars: 0 - Forks: 0

kumaranu/DrugDiscMDConformers

A python package to generate conformers for small molecules using molecular dynamics.

Language: Python - Size: 3.01 MB - Last synced: 7 days ago - Pushed: 8 days ago - Stars: 0 - Forks: 0

mojaie/MolecularGraph.jl

Graph-based molecule modeling toolkit for cheminformatics

Language: Julia - Size: 3.78 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 185 - Forks: 27

jhylin/ML2-1_decision_tree

Machine learning series 2.1 on decision tree, with information about series 1 on logistic regression

Language: Jupyter Notebook - Size: 753 KB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 1 - Forks: 0

epam/Indigo

Universal cheminformatics toolkit, utilities and database search tools

Language: C++ - Size: 221 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 277 - Forks: 98

hsiaoyi0504/awesome-cheminformatics

A curated list of Cheminformatics libraries and software.

Size: 141 KB - Last synced: 3 days ago - Pushed: 2 months ago - Stars: 642 - Forks: 107

mcocdawc/chemcoord

A python module for manipulating cartesian and internal coordinates.

Language: Python - Size: 4.55 MB - Last synced: 6 days ago - Pushed: 9 days ago - Stars: 67 - Forks: 18

awslabs/dgl-lifesci

Python package for graph neural networks in chemistry and biology

Language: Python - Size: 963 KB - Last synced: 7 days ago - Pushed: 7 months ago - Stars: 686 - Forks: 144

pnnl/cactus

LLM Agent that leverages cheminformatics tools to provide informed responses.

Language: Jupyter Notebook - Size: 14.5 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 2 - Forks: 0

benb111/awesome-small-molecule-ml

A curated list of resources for machine learning for small-molecule drug discovery

Size: 102 KB - Last synced: 3 days ago - Pushed: 6 months ago - Stars: 176 - Forks: 27

Steinbeck-Lab/cheminformatics-microservice

This set of essential and valuable microservices is designed to be accessed via API calls to support cheminformatics.

Language: Python - Size: 7.56 MB - Last synced: 9 days ago - Pushed: 10 days ago - Stars: 20 - Forks: 3

doyle-lab-ucla/auto-qchem

Auto-QChem is an automated workflow for the generation and storage of DFT calculations for organic molecules.

Language: Python - Size: 9.12 MB - Last synced: 4 days ago - Pushed: 16 days ago - Stars: 77 - Forks: 14

mims-harvard/TDC

Therapeutics Commons: Artificial Intelligence Foundation for Therapeutic Science

Language: Jupyter Notebook - Size: 67.6 MB - Last synced: 15 days ago - Pushed: 15 days ago - Stars: 930 - Forks: 167

scipion-chem/scipion-chem-lephar

Plugin for LePhar docking software

Language: Python - Size: 140 KB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 0 - Forks: 0

CDDLeiden/DrugEx

De Novo Drug Design with RNNs and Transformers

Language: Jupyter Notebook - Size: 61.9 MB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 98 - Forks: 13

mcs07/ChemSpiPy Fork of cameronneylon/ChemSpiPy

Python wrapper for the ChemSpider API

Language: Python - Size: 263 KB - Last synced: about 8 hours ago - Pushed: over 5 years ago - Stars: 109 - Forks: 27

qmlcode/qmllib

Quantum machine learning (QML) Core Fortran Functions

Language: Fortran - Size: 15.2 MB - Last synced: 11 days ago - Pushed: about 1 month ago - Stars: 6 - Forks: 1

chemosim-lab/ProLIF

Interaction Fingerprints for protein-ligand complexes and more

Language: Python - Size: 6.53 MB - Last synced: 6 days ago - Pushed: 2 months ago - Stars: 323 - Forks: 63

MolecularAI/REINVENT4

AI molecular design tool for de novo design, scaffold hopping, R-group replacement, linker design and molecule optimization.

Language: Python - Size: 1.24 GB - Last synced: 11 days ago - Pushed: 20 days ago - Stars: 222 - Forks: 53

enveda/plant-chemical-space

Source code and data for "Exploring the known chemical space of the plant kingdom: Insights into taxonomic patterns, knowledge gaps, and bioactive regions"

Language: Jupyter Notebook - Size: 23.1 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 1 - Forks: 2

maximskorik/ChemnameNormalizer

Unify and normalize names of chemical compounds via PubChem compound database.

Language: Python - Size: 33.2 KB - Last synced: 13 days ago - Pushed: about 2 years ago - Stars: 1 - Forks: 0

jhylin/Data_in_life_blog

Cheminformatics & pharmaceutical research blog

Language: HTML - Size: 140 MB - Last synced: 14 days ago - Pushed: 14 days ago - Stars: 0 - Forks: 0

jhylin/ML2-2_random_forest

Machine learning series 2.2 on random forest

Language: Jupyter Notebook - Size: 2.82 MB - Last synced: 14 days ago - Pushed: 14 days ago - Stars: 1 - Forks: 0

MolecularAI/aizynthfinder

A tool for retrosynthetic planning

Language: Python - Size: 3.73 MB - Last synced: 11 days ago - Pushed: 16 days ago - Stars: 536 - Forks: 124

cthoyt/resume

The résumé of Charles Tapley Hoyt

Language: TeX - Size: 4.15 MB - Last synced: 14 days ago - Pushed: 14 days ago - Stars: 0 - Forks: 0

Mateus-RB/MoleKing

MoleKing is a python module for chemists aiming to add common principles to python. This module adds new types of python variables, MoleKing_Molecule; MoleKing_Atom; MoleKing_SupraMolecule, and MoleKing_Output, alongside many features considered common knowledge among chemists.

Language: C++ - Size: 2.45 MB - Last synced: 13 days ago - Pushed: 14 days ago - Stars: 1 - Forks: 0

CDDLeiden/QSPRpred

A tool for creating Quantitative Structure Property Relationship (QSPR) models.

Language: Jupyter Notebook - Size: 52.6 MB - Last synced: 5 days ago - Pushed: about 1 month ago - Stars: 31 - Forks: 7

ARY2260/openpom

Replication of the Principal Odor Map paper by Brian K. Lee et al. (2023).

Language: Jupyter Notebook - Size: 22.3 MB - Last synced: 14 days ago - Pushed: about 2 months ago - Stars: 18 - Forks: 23

scipipe/scipipe

Robust, flexible and resource-efficient pipelines using Go and the commandline

Language: Go - Size: 1.05 MB - Last synced: 10 days ago - Pushed: 10 months ago - Stars: 1,053 - Forks: 72

a-r-j/DrugTranslatoR

R package for translating between drug identifiers using the Chemical Translation Service (CTS)

Language: R - Size: 6.84 KB - Last synced: 15 days ago - Pushed: over 1 year ago - Stars: 3 - Forks: 2

Pomog/Chemlabtracker

electronic laboratory notebook

Language: Java - Size: 5.93 MB - Last synced: 15 days ago - Pushed: almost 1 year ago - Stars: 2 - Forks: 0

TheRealSalmon/cheminformatics-streamlit

Interactive cheminformatics tutorials on streamlit.

Language: Python - Size: 142 KB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 3 - Forks: 0

chembl/chembl_multitask_model

Target prediction multitask neural network, with examples running it in Python, C++, Julia and JS

Language: Python - Size: 75.8 MB - Last synced: 15 days ago - Pushed: 15 days ago - Stars: 11 - Forks: 6

ATOMScience-org/AMPL

The ATOM Modeling PipeLine (AMPL) is an open-source, modular, extensible software pipeline for building and sharing models to advance in silico drug discovery.

Language: Jupyter Notebook - Size: 218 MB - Last synced: about 19 hours ago - Pushed: 1 day ago - Stars: 129 - Forks: 59

edualb/godmitri

This project provides utilities for chemistry. The name of the project was inspired by periodic table creator Dmitri Ivanovic Mendeleev name.

Language: Go - Size: 151 KB - Last synced: 15 days ago - Pushed: over 3 years ago - Stars: 3 - Forks: 0

InCogNiTo124/chemeq

Chemical equation balancer

Language: Python - Size: 6.84 KB - Last synced: 15 days ago - Pushed: over 2 years ago - Stars: 4 - Forks: 0

dewberryants/asciiMol

Curses based ASCII molecule viewer for terminals.

Language: Python - Size: 810 KB - Last synced: 2 days ago - Pushed: 12 months ago - Stars: 350 - Forks: 12

k-ujihara/NCDK

The Chemistry Development Kit ported to .NET

Language: C# - Size: 50.8 MB - Last synced: 17 days ago - Pushed: about 1 year ago - Stars: 34 - Forks: 12

wjm41/molplotly

add-on to plotly which show molecule images on mouseover!

Language: Python - Size: 17 MB - Last synced: 6 days ago - Pushed: about 1 month ago - Stars: 230 - Forks: 24

MolecularAI/Reinvent 📦

Language: Python - Size: 118 MB - Last synced: 11 days ago - Pushed: 7 months ago - Stars: 332 - Forks: 107

MolecularAI/ReinventCommunity 📦

Language: Jupyter Notebook - Size: 593 MB - Last synced: 11 days ago - Pushed: about 2 years ago - Stars: 146 - Forks: 56

AmirJlr/Molecular-Property-Prediction

Collection of Machine Learning and GNN methods for Molecular Property Prediction Task

Language: Jupyter Notebook - Size: 16.4 MB - Last synced: 18 days ago - Pushed: 18 days ago - Stars: 0 - Forks: 0

cansyl/DEEPScreen

DEEPScreen: Virtual Screening with Deep Convolutional Neural Networks Using Compound Images

Language: Python - Size: 266 MB - Last synced: 18 days ago - Pushed: 18 days ago - Stars: 107 - Forks: 40

Mishima-syk/psikit

psi4+RDKit

Language: Python - Size: 799 KB - Last synced: 13 days ago - Pushed: over 1 year ago - Stars: 92 - Forks: 18

samoturk/mol2vec 📦

Mol2vec - an unsupervised machine learning approach to learn vector representations of molecular substructures

Language: Python - Size: 86.6 MB - Last synced: 10 days ago - Pushed: over 1 year ago - Stars: 245 - Forks: 105

xduan7/MoReL

Molecule Representation Learning Toolkit

Language: Jupyter Notebook - Size: 3.88 MB - Last synced: 19 days ago - Pushed: almost 5 years ago - Stars: 4 - Forks: 2

rdkit/rdkit-js

A powerful cheminformatics and molecule rendering toolbelt for JavaScript, powered by RDKit .

Language: Dockerfile - Size: 16.4 MB - Last synced: 15 days ago - Pushed: 15 days ago - Stars: 121 - Forks: 36

Acylation/obsidian-chem

Chemistry support for Obsidian. Rendering SMILES strings into chemistry structures.

Language: TypeScript - Size: 282 KB - Last synced: 19 days ago - Pushed: 20 days ago - Stars: 61 - Forks: 5

mcsorkun/ChemPlot

A python package for chemical space visualization.

Language: Jupyter Notebook - Size: 60.2 MB - Last synced: 19 days ago - Pushed: 12 months ago - Stars: 97 - Forks: 26

scbirlab/schemist

⬢⬢⬢ Organizing and processing tables of chemical structures.

Language: Python - Size: 198 KB - Last synced: 19 days ago - Pushed: 20 days ago - Stars: 0 - Forks: 0