Mass spectrometry and the cellular surfaceome

J Pauwels, D Fijałkowska, S Eyckerman… - Mass spectrometry …, 2022 - Wiley Online Library
The collection of exposed plasma membrane proteins, collectively termed the surfaceome, is
involved in multiple vital cellular processes, such as the communication of cells with their …

Proteins: sequence to structure and function-current status

SR Shenoy, B Jayaram - Current Protein and Peptide Science, 2010 - ingentaconnect.com
In an era that has been dominated by Structural Biology for the last 30-40 years, a dramatic
change of focus towards sequence analysis has spurred the advent of the genome projects …

PDBTM: Protein Data Bank of transmembrane proteins after 8 years

D Kozma, I Simon, GE Tusnady - Nucleic acids research, 2012 - academic.oup.com
The PDBTM database (available at http://pdbtm. enzim. hu), the first comprehensive and up-
to-date transmembrane protein selection of the Protein Data Bank, was launched in 2004 …

Prediction of transporter targets using efficient RBF networks with PSSM profiles and biochemical properties

SA Chen, YY Ou, TY Lee, MM Gromiha - Bioinformatics, 2011 - academic.oup.com
Transporters are proteins that are involved in the movement of ions or molecules across
biological membranes. Currently, our knowledge about the functions of transporters is …

MPAD: A Database for Binding Affinity of Membrane Protein–protein Complexes and their Mutants

F Ridha, A Kulandaisamy, MM Gromiha - Journal of Molecular Biology, 2023 - Elsevier
Membrane protein complexes are crucial for a large variety of biological functions which are
mainly dictated by their binding affinity. Due to the intricate nature of their structure, however …

Bioinformatics approaches for functional annotation of membrane proteins

MM Gromiha, YY Ou - Briefings in bioinformatics, 2014 - academic.oup.com
Membrane proteins perform diverse functions in living organisms such as transporters,
receptors and channels. The functions of membrane proteins have been investigated with …

OMPdb: a database of β-barrel outer membrane proteins from Gram-negative bacteria

KD Tsirigos, PG Bagos… - Nucleic acids research, 2010 - academic.oup.com
We describe here OMPdb, which is currently the most complete and comprehensive
collection of integral β-barrel outer membrane proteins from Gram-negative bacteria. The …

MPTherm: database for membrane protein thermodynamics for understanding folding and stability

A Kulandaisamy, R Sakthivel… - Briefings in …, 2021 - academic.oup.com
The functions of membrane proteins (MPs) are attributed to their structure and stability.
Factors influencing the stability of MPs differ from globular proteins due to the presence of …

Predicting protein-ATP binding sites from primary sequence through fusing bi-profile sampling of multi-view features

YN Zhang, DJ Yu, SS Li, YX Fan, Y Huang, HB Shen - Bmc Bioinformatics, 2012 - Springer
Abstract Background Adenosine-5′-triphosphate (ATP) is one of multifunctional
nucleotides and plays an important role in cell biology as a coenzyme interacting with …

MutHTP: mutations in human transmembrane proteins

A Kulandaisamy, S Binny Priya, R Sakthivel… - …, 2018 - academic.oup.com
Motivation Existing sources of experimental mutation data do not consider the structural
environment of amino acid substitutions and distinguish between soluble and membrane …