Therapeutic peptide development revolutionized: Harnessing the power of artificial intelligence for drug discovery

S Hashemi, P Vosough, S Taghizadeh… - Heliyon, 2024 - cell.com
Due to the spread of antibiotic resistance, global attention is focused on its inhibition and the
expansion of effective medicinal compounds. The novel functional properties of peptides …

Computational Approaches to Predict Protein–Protein Interactions in Crowded Cellular Environments

G Grassmann, M Miotto, F Desantis… - Chemical …, 2024 - ACS Publications
Investigating protein–protein interactions is crucial for understanding cellular biological
processes because proteins often function within molecular complexes rather than in …

A structure-based data set of protein-peptide affinities and its nonredundant benchmark: potential applications in computational peptidology

S Wang, H Ye, S Shang, Z Li, Y Peng… - Current Medicinal …, 2024 - benthamdirect.com
Background: Peptides play crucial roles in diverse cellular functions and participate in many
biological processes by interacting with a variety of proteins, which have also been exploited …

Deep learning-based method for predicting and classifying the binding affinity of protein-protein complexes

R Nikam, K Yugandhar, MM Gromiha - Biochimica et Biophysica Acta (BBA) …, 2023 - Elsevier
Protein-protein interactions (PPIs) play a critical role in various biological processes.
Accurately estimating the binding affinity of PPIs is essential for understanding the …

Machine learning methods for protein-protein binding affinity prediction in protein design

Z Guo, R Yamaguchi - Frontiers in Bioinformatics, 2022 - frontiersin.org
Protein-protein interactions govern a wide range of biological activity. A proper estimation of
the protein-protein binding affinity is vital to design proteins with high specificity and binding …

Targeting protein-protein interactions with low molecular weight and short peptide modulators: insights on disease pathways and starting points for drug discovery

D Trisciuzzi, BO Villoutreix, L Siragusa… - Expert Opinion on …, 2023 - Taylor & Francis
ABSTRACT Introduction Protein-protein interactions (PPIs) have been often considered
undruggable targets although they are attractive for the discovery of new therapeutics. The …

Towards rational computational peptide design

L Chang, A Mondal, A Perez - Frontiers in Bioinformatics, 2022 - frontiersin.org
Peptides are prevalent in biology, mediating as many as 40% of protein-protein interactions,
and involved in other cellular functions such as transport and signaling. Their ability to bind …

[HTML][HTML] Accelerating therapeutic protein design with computational approaches toward the clinical stage

Z Chen, X Wang, X Chen, J Huang, C Wang… - Computational and …, 2023 - Elsevier
Therapeutic protein, represented by antibodies, is of increasing interest in human medicine.
However, clinical translation of therapeutic protein is still largely hindered by different …

Unlocking novel therapies: Cyclic peptide design for amyloidogenic targets through synergies of experiments, simulations, and machine learning

D de Raffele, IM Ilie - Chemical Communications, 2024 - pubs.rsc.org
Existing therapies for neurodegenerative diseases like Parkinson's and Alzheimer's address
only their symptoms and do not prevent disease onset. Common therapeutic agents, such as …

TopBP1 utilises a bipartite GINS binding mode to support genome replication

M Day, B Tetik, M Parlak, Y Almeida-Hernández… - Nature …, 2024 - nature.com
Activation of the replicative Mcm2-7 helicase by loading GINS and Cdc45 is crucial for
replication origin firing, and as such for faithful genetic inheritance. Our biochemical and …