Exploring protein functions from structural flexibility using CABS‐flex modeling

C Nithin, RP Fornari, SP Pilla, K Wroblewski… - Protein …, 2024 - Wiley Online Library
Understanding protein function often necessitates characterizing the flexibility of protein
structures. However, simulating protein flexibility poses significant challenges due to the …

PEP-FOLD4: a pH-dependent force field for peptide structure prediction in aqueous solution

J Rey, S Murail, S de Vries, P Derreumaux… - Nucleic Acids …, 2023 - academic.oup.com
Accurate and fast structure prediction of peptides of less 40 amino acids in aqueous solution
has many biological applications, but their conformations are pH-and salt concentration …

Protein docking model evaluation by graph neural networks

X Wang, ST Flannery, D Kihara - Frontiers in Molecular Biosciences, 2021 - frontiersin.org
Physical interactions of proteins play key functional roles in many important cellular
processes. To understand molecular mechanisms of such functions, it is crucial to determine …

Bioactive peptides from beans with the potential to decrease the risk of developing noncommunicable chronic diseases

B de Fátima Garcia, M de Barros… - Critical reviews in food …, 2021 - Taylor & Francis
Several studies have demonstrated that peptides obtained from the proteins of different
bean species have the potential to act on therapeutic targets of noncommunicable chronic …

Structure of the SHOC2–MRAS–PP1C complex provides insights into RAF activation and Noonan syndrome

DA Bonsor, P Alexander, K Snead, N Hartig… - Nature structural & …, 2022 - nature.com
SHOC2 acts as a strong synthetic lethal interactor with MEK inhibitors in multiple KRAS
cancer cell lines. SHOC2 forms a heterotrimeric complex with MRAS and PP1C that is …

New peptides with immunomodulatory activity identified from rice proteins through peptidomic and in silico analysis

L Wen, L Huang, Y Li, Y Feng, Z Zhang, Z Xu, ML Chen… - Food Chemistry, 2021 - Elsevier
The new food-derived bio-functional peptides are urgently needed globally, but the
separation and purification process for obtaining the immunopeptides from food is low …

Universal peptide-based potential vaccine design against canine distemper virus (CDV) using a vaccinomic approach

S Rendon-Marin, J Ruíz-Saenz - Scientific Reports, 2024 - nature.com
Canine distemper virus (CDV) affects many domestic and wild animals. Variations among
CDV genome linages could lead to vaccination failure. To date, there are several vaccine …

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 …

Structure prediction of linear and cyclic peptides using CABS-flex

A Badaczewska-Dawid, K Wróblewski… - Briefings in …, 2024 - academic.oup.com
The structural modeling of peptides can be a useful aid in the discovery of new drugs and a
deeper understanding of the molecular mechanisms of life. Here we present a novel …

Matching protein surface structural patches for high-resolution blind peptide docking

A Khramushin, Z Ben-Aharon… - Proceedings of the …, 2022 - National Acad Sciences
Peptide docking can be perceived as a subproblem of protein–protein docking. However,
due to the short length and flexible nature of peptides, many do not adopt one defined …