Undetected overfitting can occur when there are significant redundancies between training and validation data. We describe AVE, a new measure of training-validation redundancy for ligand-based classification problems that accounts for the similarity amongst inactive molecules as well as active. We investigated seven wi…
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10 results for “ligand-based”
Unified model learns from proteins and ligands for drug design.
problem Disjoint data sources and modeling assumptions limit joint use of structure- and ligand-based drug design.
method Contrastive Geometric Learning for Unified Computational Drug Design (ConGLUDe)
result Unified model achieves competitive zero-shot virtual screening performance and state-of-the-art ligand-conditioned pocket selection.
A novel methodology on distributed representations of proteins using their interacting ligandsstat.ML
The effective representation of proteins is a crucial task that directly affects the performance of many bioinformatics problems. Related proteins usually bind to similar ligands. Chemical characteristics of ligands are known to capture the functional and mechanistic properties of proteins suggesting that a ligand base…
Calibrated Boosting-Foreststat.ML
Excellent ranking power along with well calibrated probability estimates are needed in many classification tasks. In this paper, we introduce a technique, Calibrated Boosting-Forest that captures both. This novel technique is an ensemble of gradient boosting machines that can support both continuous and binary labels. …
Molecular "fingerprints" encoding structural information are the workhorse of cheminformatics and machine learning in drug discovery applications. However, fingerprint representations necessarily emphasize particular aspects of the molecular structure while ignoring others, rather than allowing the model to make data-d…
Deep learning methods such as multitask neural networks have recently been applied to ligand-based virtual screening and other drug discovery applications. Using a set of industrial ADMET datasets, we compare neural networks to standard baseline models and analyze multitask learning effects with both random cross-valid…
Large-scale ligand-based virtual screening for SARS-CoV-2 inhibitors using deep neural networksq-bio.BM
Deep neural network identifies potential SARS-CoV-2 inhibitors.
problem Finding novel therapies for SARS-CoV-2.
method Used ChemAI, a deep neural network trained on 220M data points, to screen and rank one billion molecules from the ZINC database.
result Identified 30,000 top-ranked compounds for further bioassays.
Deep convolutional neural networks comprise a subclass of deep neural networks (DNN) with a constrained architecture that leverages the spatial and temporal structure of the domain they model. Convolutional networks achieve the best predictive performance in areas such as speech and image recognition by hierarchically …
New method uses Riemannian geometry to describe molecular shapes.
problem Predicting drug-like molecules using shape similarity.
method Riemannian geometry applied to molecular surfaces.
result RGMolSA method captures molecular shape effectively.
According to Cobanoglu et al and Murphy, it is now widely acknowledged that the single target paradigm (one protein or target, one disease, one drug) that has been the dominant premise in drug development in the recent past is untenable. More often than not, a drug-like compound (ligand) can be promiscuous - that is, i…