Computational methods and tools for binding site recognition between proteins and small molecules: from classical geometrical approaches to modern machine …

G Macari, D Toti, F Polticelli - Journal of computer-aided molecular design, 2019 - Springer
In the current “genomic era” the number of identified genes is growing exponentially.
However, the biological function of a large number of the corresponding proteins is still …

Bioinformatics calls the school: Use of smartphones to introduce Python for bioinformatics in high schools

AJ Velez Rueda, GI Benítez, J Marchetti… - PLoS computational …, 2019 - journals.plos.org
The dynamic nature of technological developments invites us to rethink the learning spaces.
In this context, science education can be enriched by the contribution of new computational …

[HTML][HTML] YAC tripeptide of epidermal growth factor promotes the proliferation of HaCaT keratinocytes through activation of EGFR

YH Yoo, YR Kim, MS Kim, KJ Lee, KH Park… - BMB reports, 2014 - ncbi.nlm.nih.gov
Epidermal growth factor (EGF) is known to play key roles in skin regeneration and wound-
healing. Here, we demonstrate that Pep2-YAC, a tripeptide covering residues 29-31 in the B …

Binding of single-mutant epidermal growth factor (EGF) ligands alters the stability of the EGF receptor dimer and promotes growth signaling

S Pascarelli, D Merzhakupova, GI Uechi… - Journal of Biological …, 2021 - ASBMB
The epidermal growth factor receptor (EGFR) is a membrane-anchored tyrosine kinase that
is able to selectively respond to multiple extracellular stimuli. Previous studies have …

Ensemble Architecture for Prediction of Enzyme‐ligand Binding Residues Using Evolutionary Information

PP Pai, RK Dattatreya, S Mondal - Molecular Informatics, 2017 - Wiley Online Library
Enzyme interactions with ligands are crucial for various biochemical reactions governing life.
Over many years attempts to identify these residues for biotechnological manipulations have …

Optimization of sequence alignments according to the number of sequences vs. number of sites trade-off

JY Dutheil, E Figuet - BMC bioinformatics, 2015 - Springer
Background Comparative analysis of homologous sequences enables the understanding of
evolutionary patterns at the molecular level, unraveling the functional constraints that …

[PDF][PDF] Protein Sequence, Structure, and Dynamics Reveal Insights in the Divergence of Protein Functions

S Pascarelli - 2023 - oist.repo.nii.ac.jp
Proteins participate in every important aspect of known living systems. The amino acid
sequence of a protein contains information about the physicochemical properties, the …

Function prediction using patches, pockets and other surface properties

DJ Rigden - From Protein Structure to Function with Bioinformatics, 2017 - Springer
With few exceptions protein functions depend sensitively upon their interactions with other
biomolecules. Thus, the surface of a protein is of particular interest for function annotation …

[PDF][PDF] Single EGF mutants unravel the mechanism for stabilization of Epidermal Growth Factor Receptor (EGFR) system

S Pascarelli, D Merzhakupova, GI Uechi, P Laurino - bioRxiv, 2020 - scholar.archive.org
The Epidermal Growth Factor Receptor (EGFR) is a membrane-anchored tyrosine kinase
that 19 is able to respond to multiple extra-cellular stimuli in a selective way. Previous …

[PDF][PDF] Protein interactions of epithelial neutral amino acid transporters

S Fairweather - 2017 - core.ac.uk
Neutral amino acids are essential for protein synthesis, energy homeostasis, and many vital
biochemical pathways. As several neutral amino acids are essential and cannot be …