An overview of recent advances in structural bioinformatics of protein–protein interactions and a guide to their principles

G Sudha, R Nussinov, N Srinivasan - Progress in biophysics and molecular …, 2014 - Elsevier
Rich data bearing on the structural and evolutionary principles of protein–protein
interactions are paving the way to a better understanding of the regulation of function in the …

CryptoSite: expanding the druggable proteome by characterization and prediction of cryptic binding sites

P Cimermancic, P Weinkam, TJ Rettenmaier… - Journal of molecular …, 2016 - Elsevier
Many proteins have small-molecule binding pockets that are not easily detectable in the
ligand-free structures. These cryptic sites require a conformational change to become …

Computational and biochemical characterization of two partially overlapping interfaces and multiple weak-affinity K-Ras dimers

P Prakash, A Sayyed-Ahmad, KJ Cho, DM Dolino… - Scientific reports, 2017 - nature.com
Recent studies found that membrane-bound K-Ras dimers are important for biological
function. However, the structure and thermodynamic stability of these complexes remained …

Specificity and stability of transient protein–protein interactions

S Vishwanath, A Sukhwal, R Sowdhamini… - Current Opinion in …, 2017 - Elsevier
Highlights•Specificity and stability are two major determinants of protein recognition in
transient protein–protein complexes (tPPCs).•Some interface residues of tPPCs are rigid in …

Deciphering Isoniazid Drug Resistance Mechanisms on Dimeric Mycobacterium tuberculosis KatG via Post-molecular Dynamics Analyses Including Combined …

V Barozi, TM Musyoka, O Sheik Amamuddy… - ACS …, 2022 - ACS Publications
Resistance mutations in Mycobacterium tuberculosis (Mtb) catalase peroxidase protein
(KatG), an essential enzyme in isoniazid (INH) activation, reduce the sensitivity of Mtb to first …

Structural and dynamics aspects of ASC speck assembly

AC Sahillioglu, F Sumbul, N Ozoren, T Haliloglu - Structure, 2014 - cell.com
Activation of the inflammasome is accompanied by rapid formation of a micrometer-sized
perinuclear structure called the ASC speck, a platform for caspase-1 activity. The ASC speck …

Learning protein binding affinity using privileged information

WA Abbasi, A Asif, A Ben-Hur, FAA Minhas - BMC bioinformatics, 2018 - Springer
Background Determining protein-protein interactions and their binding affinity are important
in understanding cellular biological processes, discovery and design of novel therapeutics …

Protein–protein interaction interfaces and their functional implications

G Schreiber - 2020 - books.rsc.org
Proteins are extremely heterogenous molecules, which allows them to execute such a large
variety of biological functions. Proteins have structural roles, perform chemical catalysis and …

Interface residues of transient protein-protein complexes have extensive intra-protein interactions apart from inter-protein interactions

S Jayashree, P Murugavel, R Sowdhamini… - Biology direct, 2019 - Springer
Background Protein-protein interactions are crucial for normal biological processes and to
regulate cellular reactions that affect gene expression and function. Several previous studies …

Tertiary structure-based prediction of conformational B-cell epitopes through B factors

J Ren, Q Liu, J Ellis, J Li - Bioinformatics, 2014 - academic.oup.com
Motivation: B-cell epitope is a small area on the surface of an antigen that binds to an
antibody. Accurately locating epitopes is of critical importance for vaccine development …