Open-source machine learning in computational chemistry

A Hagg, KN Kirschner - Journal of Chemical Information and …, 2023 - ACS Publications
The field of computational chemistry has seen a significant increase in the integration of
machine learning concepts and algorithms. In this Perspective, we surveyed 179 open …

[HTML][HTML] Integrative modelling of biomolecular complexes

PI Koukos, A Bonvin - Journal of molecular biology, 2020 - Elsevier
In recent years, the use of integrative, information-driven computational approaches for
modeling the structure of biomolecules has been increasing in popularity. These are now …

Antioxidant, pancreatic lipase, and α‐amylase inhibitory properties of oat bran hydrolyzed proteins and peptides

R Esfandi, I Seidu, W Willmore… - Journal of Food …, 2022 - Wiley Online Library
This work aimed to determine the antioxidant properties of identified hydrolyzed oat proteins
and peptides, and their capacity to inhibit lipase and α‐amylase. The protein hydrolysates …

[HTML][HTML] Invited review: Camel milk–derived bioactive peptides and diabetes—Molecular view and perspectives

MA Ayoub, PG Yap, P Mudgil, FB Khan, I Anwar… - Journal of Dairy …, 2024 - Elsevier
In dairy science, camel milk (CM) constitutes a center of interest for scientists due to its
known beneficial effect on diabetes as demonstrated in many in vitro, in vivo, and clinical …

Design of Cyclic Peptides Targeting Protein–Protein Interactions Using AlphaFold

T Kosugi, M Ohue - International Journal of Molecular Sciences, 2023 - mdpi.com
More than 930,000 protein–protein interactions (PPIs) have been identified in recent years,
but their physicochemical properties differ from conventional drug targets, complicating the …

MDM2‐Targeting Reassembly Peptide (TRAP) Nanoparticles for p53‐Based Cancer Therapy

F Li, D Chen, Q Sun, J Wu, Y Gan… - Advanced …, 2023 - Wiley Online Library
Gene mutations and functional inhibition are the major obstacles for p53‐mediated
oncotherapy. For p53‐wild‐type tumors, the underlying mechanisms of functional inhibition …

Flexible docking of peptides to proteins using CABS‐dock

M Kurcinski, A Badaczewska‐Dawid… - Protein …, 2020 - Wiley Online Library
Molecular docking of peptides to proteins can be a useful tool in the exploration of the
possible peptide binding sites and poses. CABS‐dock is a method for protein–peptide …

Targeting tumors using peptides

P Scodeller, EK Asciutto - Molecules, 2020 - mdpi.com
To penetrate solid tumors, low molecular weight (Mw< 10 KDa) compounds have an edge
over antibodies: their higher penetration because of their small size. Because of the dense …

Computational prediction of disordered binding regions

S Basu, D Kihara, L Kurgan - Computational and Structural Biotechnology …, 2023 - Elsevier
One of the key features of intrinsically disordered regions (IDRs) is their ability to interact
with a broad range of partner molecules. Multiple types of interacting IDRs were identified …

Integrative modeling of diverse protein-peptide systems using CABS-dock

W Puławski, A Koliński, M Koliński - PLoS Computational Biology, 2023 - journals.plos.org
The CABS model can be applied to a wide range of protein-protein and protein-peptide
molecular modeling tasks, such as simulating folding pathways, predicting structures …