[HTML][HTML] Open source molecular modeling

S Pirhadi, J Sunseri, DR Koes - Journal of Molecular Graphics and …, 2016 - Elsevier
The success of molecular modeling and computational chemistry efforts are, by definition,
dependent on quality software applications. Open source software development provides …

Evaluation of deep learning in non-coding RNA classification

N Amin, A McGrath, YPP Chen - Nature Machine Intelligence, 2019 - nature.com
Non-coding (nc) RNA plays a vital role in biological processes and has been associated
with diseases such as cancer. Classification of ncRNAs is necessary for understanding the …

Machine Learning Methods for Property Prediction in Chemoinformatics: Quo Vadis?

A Varnek, I Baskin - Journal of chemical information and modeling, 2012 - ACS Publications
This paper is focused on modern approaches to machine learning, most of which are as yet
used infrequently or not at all in chemoinformatics. Machine learning methods are …

cardioToxCSM: A Web Server for Predicting Cardiotoxicity of Small Molecules

S Iftkhar, AGC de Sá, JPL Velloso, R Aljarf… - Journal of Chemical …, 2022 - ACS Publications
The design of novel, safe, and effective drugs to treat human diseases is a challenging
venture, with toxicity being one of the main sources of attrition at later stages of …

Derivation and validation of novel phenotypes of multiple organ dysfunction syndrome in critically ill children

LN Sanchez-Pinto, EK Stroup, T Pendergrast… - JAMA network …, 2020 - jamanetwork.com
Importance Multiple organ dysfunction syndrome (MODS) is a dynamic and heterogeneous
process associated with high morbidity and mortality in critically ill children. Objective To …

pdCSM-cancer: using graph-based signatures to identify small molecules with anticancer properties

R Al-Jarf, AGC de Sá, DEV Pires… - Journal of Chemical …, 2021 - ACS Publications
The development of new, effective, and safe drugs to treat cancer remains a challenging and
time-consuming task due to limited hit rates, restraining subsequent development efforts …

Functional annotation of chemical libraries across diverse biological processes

JS Piotrowski, SC Li, R Deshpande… - Nature Chemical …, 2017 - nature.com
Chemical-genetic approaches offer the potential for unbiased functional annotation of
chemical libraries. Mutations can alter the response of cells in the presence of a compound …

PDCSM-PPI: Using graph-based signatures to identify protein–protein interaction inhibitors

CHM Rodrigues, DEV Pires… - Journal of Chemical …, 2021 - ACS Publications
Protein–protein interactions are promising sites for development of selective drugs;
however, they have generally been viewed as challenging targets. Molecules targeting …

nRC: non-coding RNA Classifier based on structural features

A Fiannaca, M La Rosa, L La Paglia, R Rizzo, A Urso - BioData mining, 2017 - Springer
Abstract Motivation Non-coding RNA (ncRNA) are small non-coding sequences involved in
gene expression regulation of many biological processes and diseases. The recent …

Near-optimal supervised feature selection among frequent subgraphs

M Thoma, H Cheng, A Gretton, J Han, HP Kriegel… - Proceedings of the 2009 …, 2009 - SIAM
Graph classification is an increasingly important step in numerous application domains,
such as function prediction of molecules and proteins, computerised scene analysis, and …