[HTML][HTML] Membrane proteins structures: A review on computational modeling tools

JG Almeida, AJ Preto, PI Koukos, AMJJ Bonvin… - … et Biophysica Acta (BBA …, 2017 - Elsevier
Abstract Background Membrane proteins (MPs) play diverse and important functions in
living organisms. They constitute 20% to 30% of the known bacterial, archaean and …

Computational modeling of membrane proteins

J Koehler Leman, MB Ulmschneider… - … Structure, Function, and …, 2015 - Wiley Online Library
The determination of membrane protein (MP) structures has always trailed that of soluble
proteins due to difficulties in their overexpression, reconstitution into membrane mimetics …

Prediction of membrane transport proteins and their substrate specificities using primary sequence information

NK Mishra, J Chang, PX Zhao - PloS one, 2014 - journals.plos.org
Background Membrane transport proteins (transporters) move hydrophilic substrates across
hydrophobic membranes and play vital roles in most cellular functions. Transporters …

[HTML][HTML] Computational studies of membrane proteins: models and predictions for biological understanding

J Liang, H Naveed, D Jimenez-Morales… - … et Biophysica Acta (BBA …, 2012 - Elsevier
We discuss recent progresses in computational studies of membrane proteins based on
physical models with parameters derived from bioinformatics analysis. We describe …

Predicting helix–helix interactions from residue contacts in membrane proteins

A Lo, YY Chiu, EA Rødland, PC Lyu, TY Sung… - …, 2009 - academic.oup.com
Motivation: Helix–helix interactions play a critical role in the structure assembly, stability and
function of membrane proteins. On the molecular level, the interactions are mediated by one …

TopProperty: Robust metaprediction of transmembrane and globular protein features using deep neural networks

D Mulnaes, S Schott-Verdugo, F Koenig… - Journal of chemical …, 2021 - ACS Publications
Transmembrane proteins (TMPs) are critical components of cellular life. However, due to
experimental challenges, the number of experimentally resolved TMP structures is severely …

Not all transmembrane helices are born equal: Towards the extension of the sequence homology concept to membrane proteins

WC Wong, S Maurer-Stroh, F Eisenhaber - Biology direct, 2011 - Springer
Background Sequence homology considerations widely used to transfer functional
annotation to uncharacterized protein sequences require special precautions in the case of …

Prediction and targeting of GPCR oligomer interfaces

CAV Barreto, SJ Baptista, AJ Preto… - Progress in molecular …, 2020 - Elsevier
GPCR oligomerization has emerged as a hot topic in the GPCR field in the last years.
Receptors that are part of these oligomers can influence each other's function, although it is …

Prediction and targeting of interaction interfaces in G-protein coupled receptor oligomers

AC Schiedel, M Kose, C Barreto… - Current topics in …, 2018 - ingentaconnect.com
Background: Communication within a protein complex is mediated by physical interactions
made among the protomers. Evidence for both the allosteric regulation present among the …

Prediction enhancement of residue real-value relative accessible surface area in transmembrane helical proteins by solving the output preference problem of machine …

F Xiao, HB Shen - Journal of chemical information and modeling, 2015 - ACS Publications
The α-helical transmembrane proteins constitute 25% of the entire human proteome space
and are difficult targets in high-resolution wet-lab structural studies, calling for accurate …