PepFun: open source protocols for peptide-related computational analysis

R Ochoa, P Cossio - Molecules, 2021 - mdpi.com
Peptide research has increased during the last years due to their applications as
biomarkers, therapeutic alternatives or as antigenic sub-units in vaccines. The …

[HTML][HTML] Assessing the fast prediction of peptide conformers and the impact of non-natural modifications

R Ochoa, T Fox - Journal of Molecular Graphics and Modelling, 2023 - Elsevier
We present an assessment of different approaches to predict peptide structures using
modeling tools. Several small molecule, protein, and peptide-focused methodologies were …

In-vitro and in-silico analyses of the thrombolytic potential of green kiwifruit

R Pinontoan, JS Purnomo, EB Avissa, JP Tanojo… - Scientific Reports, 2024 - nature.com
Cardiovascular diseases (CVDs), mainly caused by thrombosis complications, are the
leading cause of mortality worldwide, making the development of alternative treatments …

The CABANA model 2017–2022: research and training synergy to facilitate bioinformatics applications in Latin America

R Campos-Sánchez, I Willis, P Gopalasingam… - Frontiers in …, 2024 - frontiersin.org
The CABANA project (Capacity Building for Bioinformatics in Latin America) was funded by
the UK's Global Challenges Research Fund in 2017 with the aim to strengthen the …

Protocol for iterative optimization of modified peptides bound to protein targets

R Ochoa, P Cossio, T Fox - Journal of Computer-Aided Molecular Design, 2022 - Springer
Peptides are commonly used as therapeutic agents. However, they suffer from easy
degradation and instability. Replacing natural by non-natural amino acids can avoid these …

Prediction of viral protease inhibitors using proteochemometrics approach

DA Karasev, BN Sobolev, DA Filimonov… - … Biology and Chemistry, 2024 - Elsevier
Being widely accepted tools in computational drug search, the (Q) SAR methods have
limitations related to data incompleteness. The proteochemometrics (PCM) approach …

Embracing enzyme promiscuity with activity-based compressed biosensing

BA Holt, HS Lim, A Sivakumar, H Phuengkham… - Cell Reports …, 2023 - cell.com
The development of protease-activatable drugs and diagnostics requires identifying
substrates specific to individual proteases. However, this process becomes increasingly …

[HTML][HTML] Open protocols for docking and MD-based scoring of peptide substrates

R Ochoa, Á Santiago, M Alegría-Arcos - Artificial Intelligence in the Life …, 2022 - Elsevier
The study of protein-peptide interactions is an active research field from an experimental
and computational perspective, with the latest presenting challenges to model and simulate …

[PDF][PDF] Artificial Intelligence in the Life Sciences

R Ochoa, Á Santiago, M Alegría-Arcos - researchgate.net
abstract The study of protein-peptide interactions is an active research field from an
experimental and computational perspective, with the latest presenting challenges to model …

[PDF][PDF] Protocol for the Computational Optimization of Modified Peptides as Potential Protease Inhibitors

R Ochoa, P Cossio - kvinzo.com
From the repertoire of targets, enzymes interacting with peptide substrates constitutes one of
the most interesting groups to block due to their impact as key drivers in many biological …