Peptides mediate up to 40% of protein interactions, their high specificity and ability to bind in places where small molecules cannot make them potential drug candidates. However, predicting peptide-protein complexes remains more challenging than protein-protein or protein-small molecule interactions, in part due to the high flexibility peptides have. In this review, we look at the advances in docking, molecular simulations and machine learning to tackle problems related to peptides such as predicting structures, binding affinities or even kinetics. We specifically focus on explaining the number of docking programmes and force fields used in molecular simulations, so a prospective user can have an educated guess as to why choose one modelling tool or another to address their scientific questions.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10392694 | PMC |
| http://dx.doi.org/10.1017/qrd.2022.14 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
AMPed up immunity: 418 whole genomes reveal intraspecific diversity of koala antimicrobial peptides.
Immunogenetics
January 2025
School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia.
Characterising functional diversity is a vital element to understanding a species' immune function, yet many immunogenetic studies in non-model organisms tend to focus on only one or two gene families such as the major histocompatibility complex (MHC) or toll-like receptors (TLR). Another interesting component of the eukaryotic innate immune system is the antimicrobial peptides (AMPs). The two major groups of mammalian AMPs are cathelicidins and defensins, with the former having undergone species-specific expansions in marsupials.
View Article and Find Full Text PDFEngineering of peptide assemblies for adaptable protein delivery to achieve efficient intracellular biocatalysis.
J Colloid Interface Sci
December 2024
State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East), 66 Changjiang West Road, Qingdao 266580, China.
Efficient intracellular delivery of native proteins remains a big challenge, which greatly hinders the development of protein therapy. Here, we report a generalizable peptide vector that can encapsulate and deliver various proteins to achieve efficient intracellular biocatalysis. The peptide was rationally designed to be cationic amphiphilic peptide that consist of four functional fragments, that is, a hydrophobic domain to promote molecular assembly, an enzyme-cleavable fragment to introduce stimuli-responsibility, several cationic arginine (Arg) residues to enhance cell interaction and transmembrane efficiency, and the cystine (Cys) residues with redox sensitivity to adjust the stability of the peptide/protein complexes as needed.
View Article and Find Full Text PDFIn Silico Design of Peptide Inhibitors Targeting HER2 for Lung Cancer Therapy.
Cancers (Basel)
November 2024
Center of Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah 22254, Saudi Arabia.
Background/objectives: Human epidermal growth factor receptor 2 (HER2) is overexpressed in several malignancies, such as breast, gastric, ovarian, and lung cancers, where it promotes aggressive tumor proliferation and unfavorable prognosis. Targeting HER2 has thus emerged as a crucial therapeutic strategy, particularly for HER2-positive malignancies. The present study focusses on the design and optimization of peptide inhibitors targeting HER2, utilizing machine learning to identify and enhance peptide candidates with elevated binding affinities.
View Article and Find Full Text PDFRendering Proteins Fluorescent Inconspicuously: Genetically Encoded 4-Cyanotryptophan Conserves Their Structure and Enables the Detection of Ligand Binding Sites.
Angew Chem Int Ed Engl
December 2024
ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
Cyanotryptophans (CN-Trp) are privileged multimodal reporters on protein structure. They are similar in size to the canonical amino acid tryptophan and some of them exhibit bright fluorescence which responds sensitively to changes in the environment. We selected aminoacyl-tRNA synthetases specific for 4-, 5-, 6-, and 7-CN-Trp for high-yield in vivo production of proteins with a single, site-specifically introduced nitrile label.
View Article and Find Full Text PDFImpact of camel milk lactoferrin peptides against breast cancer cells: and study.
Front Pharmacol
November 2024
Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
Background And Aims: Breast cancer remains a significant global health concern, necessitating the exploration of novel therapeutic strategies. Despite advancements in cancer therapeutics, effective treatments with minimal side effects remain elusive. Natural sources, such as camel milk, harbor bioactive compounds such as lactoferrin peptides, which hold promise as anticancer agents.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!