Journal of Cheminformatics's Projects
Investigation of chemical structure recognition by encoder–decoder models in learning progress (https://jcheminf.biomedcentral.com/articles/10.1186/s13321-023-00713-z)
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)
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)
An atom-bond transformer-based message passing neural network for molecular property prediction. (https://jcheminf.biomedcentral.com/articles/10.1186/s13321-023-00698-9)
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.
Learning Protein-Ligand Properties with Atomic Environment Vectors
A tool for retrosynthetic planning
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
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)
Conformers of the twenty proeinogenic aminoacids (TorsiFlex 2021.1)
Aromatic clusters in proteins
Critical assessment of synthetic accessibility scores in computer-assisted synthesis planning (https://jcheminf.biomedcentral.com/articles/10.1186/s13321-023-00678-z)
ASFP (Artificial Intelligence based Scoring Function Platform): a web server for the development of customized scoring functions
Explainable uncertainty quantifications for deep learning-based molecular property prediction (https://jcheminf.biomedcentral.com/articles/10.1186/s13321-023-00682-3)
Learning atom mappings in chemical reactions through deep graph matching (https://jcheminf.biomedcentral.com/articles/10.1186/s13321-024-00841-0)
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: enhancing chemical reaction datasets for machine learning applications in organic chemistry (https://jcheminf.biomedcentral.com/articles/10.1186/s13321-024-00869-2)
AstraZeneca add-ons to Orange.
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: 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)
Blood–Brain Barrier Penetration Prediction Enhanced by Uncertainty Estimation
Data and code of enzymatic reaction prediction model BEC-Pred. (https://jcheminf.biomedcentral.com/articles/10.1186/s13321-024-00827-y)
Code for the implementation of BERT enriched embedding, used for reaction yield prediction.(https://jcheminf.biomedcentral.com/articles/10.1186/s13321-023-00685-0)
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)
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)
Applying atomistic neural networks to bias conformer ensemble towards bioactive-like conformations (https://jcheminf.biomedcentral.com/articles/10.1186/s13321-023-00794-w)