A structural model of the active ribosome-bound membrane protein insertase YidC

S Wickles, A Singharoy, J Andreani, S Seemayer… - Elife, 2014 - elifesciences.org
The integration of most membrane proteins into the cytoplasmic membrane of bacteria
occurs co-translationally. The universally conserved YidC protein mediates this process …

Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP

J Koehler Leman, S Lyskov, R Bonneau - BMC bioinformatics, 2017 - Springer
Background Membrane proteins are underrepresented in structural databases, which has
led to a lack of computational tools and the corresponding inappropriate use of tools …

Membrane contact probability: An essential and predictive character for the structural and functional studies of membrane proteins

L Wang, J Zhang, D Wang, C Song - PLOS Computational Biology, 2022 - journals.plos.org
One of the unique traits of membrane proteins is that a significant fraction of their
hydrophobic amino acids is exposed to the hydrophobic core of lipid bilayers rather than …

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 …

Identification of 121 variants of honey bee Vitellogenin protein sequences with structural differences at functional sites

V Leipart, J Ludvigsen, M Kent, S Sandve… - Protein …, 2022 - Wiley Online Library
Proteins are under selection to maintain central functions and to accommodate needs that
arise in ever‐changing environments. The positive selection and neutral drift that preserve …

Tmp-ssurface2: a novel deep learning-based surface accessibility predictor for transmembrane protein sequence

Z Liu, Y Gong, Y Guo, X Zhang, C Lu, L Zhang… - Frontiers in …, 2021 - frontiersin.org
Transmembrane protein (TMP) is an important type of membrane protein that is involved in
various biological membranes related biological processes. As major drug targets, TMPs' …

ProtRAP: Predicting lipid accessibility together with solvent accessibility of proteins in one run

K Kang, L Wang, C Song - Journal of Chemical Information and …, 2023 - ACS Publications
Solvent accessibility has been extensively used to characterize and predict the chemical
properties of the surface residues of soluble proteins. However, there is not yet a widely …

Accurate prediction of contact numbers for multi-spanning helical membrane proteins

B Li, J Mendenhall, ED Nguyen… - Journal of chemical …, 2016 - ACS Publications
Prediction of the three-dimensional (3D) structures of proteins by computational methods is
acknowledged as an unsolved problem. Accurate prediction of important structural …

TMP-SSurface: a deep learning-based predictor for surface accessibility of transmembrane protein residues

C Lu, Z Liu, B Kan, Y Gong, Z Ma, H Wang - Crystals, 2019 - mdpi.com
Transmembrane proteins (TMPs) play vital and diverse roles in many biological processes,
such as molecular transportation and immune response. Like other proteins, many major …

Determination of hydrophobic lengths of membrane proteins with the HDGB implicit membrane model

B Dutagaci, M Feig - Journal of chemical information and …, 2017 - ACS Publications
A protocol for predicting the hydrophobic length of membrane proteins using the
heterogeneous dielectric generalized Born (HDGB) implicit membrane model is presented …