2022

Investigation of chemical structure recognition by encoder–decoder models in learning progress (https://jcheminf.biomedcentral.com/articles/10.1186/s13321-023-00713-z)

230502

A BERT-based pretraining model for extracting molecular structural information from a SMILES sequence (https://jcheminf.biomedcentral.com/articles/10.1186/s13321-024-00848-7)

3ddpd

A repository to generate 3D dynamic protein descriptors (3DDPDs) from molecular dynamics (MS) simulations for proteochemometric (PCM) modelling (https://jcheminf.biomedcentral.com/articles/10.1186/s13321-023-00745-5)

a-hiot

abt-mpnn

An atom-bond transformer-based message passing neural network for molecular property prediction. (https://jcheminf.biomedcentral.com/articles/10.1186/s13321-023-00698-9)

acid

Auto in silico Consensus Inverse Docking(ACID) is a web server mainly for drug repurposing based on the consensus inverse docking method, which is designed to evaluate the binding affinities between each protein and the given small molecule. ACID is open to the public and shows great potential.

aescore

Learning Protein-Ligand Properties with Atomic Environment Vectors

aizynthfinder

A tool for retrosynthetic planning

alpinac

amadar

Supporting "AMADAR: a python-based package for large scale prediction of Diels–Alder transition state geometries and IRC path analysis", Journal of Cheminformatics 2022, 14:39

ames-mutagenicity-optimization

Code and Data for 'Chemical Rules for Optimization of Chemical Mutagenicity via Matched Molecular Pairs Analysis and Machine Learning Methods' (https://jcheminf.biomedcentral.com/articles/10.1186/s13321-023-00707-x)

aminoacids

Conformers of the twenty proeinogenic aminoacids (TorsiFlex 2021.1)

aromatics

Aromatic clusters in proteins

asap

Critical assessment of synthetic accessibility scores in computer-assisted synthesis planning (https://jcheminf.biomedcentral.com/articles/10.1186/s13321-023-00678-z)

asfp

ASFP (Artificial Intelligence based Scoring Function Platform): a web server for the development of customized scoring functions

atom-based_uncertainty_model

Explainable uncertainty quantifications for deep learning-based molecular property prediction (https://jcheminf.biomedcentral.com/articles/10.1186/s13321-023-00682-3)

atom-matching-network

Learning atom mappings in chemical reactions through deep graph matching (https://jcheminf.biomedcentral.com/articles/10.1186/s13321-024-00841-0)

atomicchargecalculator2

augmented-xai

Using test-time augmentation to investigate explainable AI: inconsistencies between method, model and human intuition (https://jcheminf.biomedcentral.com/articles/10.1186/s13321-024-00824-1)

autotemplate

AutoTemplate: enhancing chemical reaction datasets for machine learning applications in organic chemistry (https://jcheminf.biomedcentral.com/articles/10.1186/s13321-024-00869-2)

azorange

AstraZeneca add-ons to Orange.

b17r

basic-pka-estimation-nitrogen-compounds

Reliable and accurate prediction of basic pK𝑎 values in nitrogen compounds: the pK𝑎 shift in supramolecular systems as a case study (https://jcheminf.biomedcentral.com/articles/10.1186/s13321-023-00763-3)

bbb-pep-prediction

BBB-PEP-prediction: improved computational model for identification of blood–brain barrier peptides using blending position relative composition specific features and ensemble modeling (https://jcheminf.biomedcentral.com/articles/10.1186/s13321-023-00773-1)

bbb_uncertainty_project

Blood–Brain Barrier Penetration Prediction Enhanced by Uncertainty Estimation

bec-pred

Data and code of enzymatic reaction prediction model BEC-Pred. (https://jcheminf.biomedcentral.com/articles/10.1186/s13321-024-00827-y)

bee

Code for the implementation of BERT enriched embedding, used for reaction yield prediction.(https://jcheminf.biomedcentral.com/articles/10.1186/s13321-023-00685-0)

binding-sites

Learnt representations of proteins can be used for accurate prediction of small molecule binding sites on experimentally determined and predicted protein structures (https://jcheminf.biomedcentral.com/articles/10.1186/s13321-024-00821-4)

bindiscover

The BinDiscover database: a biology-focused meta-analysis tool for 156,000 GC–TOF MS metabolome samples (https://jcheminf.biomedcentral.com/articles/10.1186/s13321-023-00734-8)

bioactive_conformation_predictor

Applying atomistic neural networks to bias conformer ensemble towards bioactive-like conformations (https://jcheminf.biomedcentral.com/articles/10.1186/s13321-023-00794-w)