Hot spots and transient pockets: predicting the determinants of small-molecule binding to a protein–protein interface

A Metz, C Pfleger, H Kopitz… - Journal of chemical …, 2012 - ACS Publications
Protein–protein interfaces are considered difficult targets for small-molecule protein–protein
interaction modulators (PPIMs). Here, we present for the first time a computational strategy …

Large-scale validation of mixed-solvent simulations to assess hotspots at protein–protein interaction interfaces

P Ghanakota, H van Vlijmen, W Sherman… - Journal of Chemical …, 2018 - ACS Publications
The ability to target protein–protein interactions (PPIs) with small molecule inhibitors offers
great promise in expanding the druggable target space and addressing a broad range of …

Computational close up on protein–protein interactions: how to unravel the invisible using molecular dynamics simulations?

C Rakers, M Bermudez, BG Keller… - Wiley …, 2015 - Wiley Online Library
As an essential part of many biological processes, protein–protein interactions (PPIs) offer
exciting and promising opportunities for drug discovery by extension of the druggable target …

Solvent Sites Improve Docking Performance of Protein–Protein Complexes and Protein–Protein Interface-Targeted Drugs

GF Mayol, LA Defelipe, JP Arcon… - Journal of Chemical …, 2022 - ACS Publications
Protein–protein interactions (PPIs) are essential, and modulating their function through PPI-
targeted drugs is an important research field. PPI sites are shallow protein surfaces readily …

How does a small molecule bind at a cryptic binding site?

Y Shan, VP Mysore, AE Leffler, ET Kim… - PLoS computational …, 2022 - journals.plos.org
Protein-protein interactions (PPIs) are ubiquitous biomolecular processes that are central to
virtually all aspects of cellular function. Identifying small molecules that modulate specific …

In silico structure-based approaches to discover protein-protein interaction-targeting drugs

WH Shin, CW Christoffer, D Kihara - Methods, 2017 - Elsevier
A core concept behind modern drug discovery is finding a small molecule that modulates a
function of a target protein. This concept has been successfully applied since the mid-1970s …

How good are state-of-the-art docking tools in predicting ligand binding modes in protein–protein interfaces?

DM Krüger, G Jessen, H Gohlke - Journal of chemical …, 2012 - ACS Publications
Protein–protein interfaces (PPIs) are an important class of drug targets. We report on the first
large-scale validation study on docking into PPIs. DrugScore-adapted AutoDock3 and Glide …

In silico-in vitro screening of protein-protein interactions: towards the next generation of therapeutics

BO Villoutreix, K Bastard, O Sperandio… - Current …, 2008 - ingentaconnect.com
Protein-protein interactions (PPIs) have a pivotal role in many biological processes
suggesting that targeting macromolecular complexes will open new avenues for the design …

Relationship between hot spot residues and ligand binding hot spots in protein–protein interfaces

BS Zerbe, DR Hall, S Vajda, A Whitty… - Journal of chemical …, 2012 - ACS Publications
In the context of protein–protein interactions, the term “hot spot” refers to a residue or cluster
of residues that makes a major contribution to the binding free energy, as determined by …

Computational method to identify druggable binding sites that target protein–protein interactions

H Li, V Kasam, CS Tautermann… - Journal of chemical …, 2014 - ACS Publications
Protein–protein interactions are implicated in the pathogenesis of many diseases and are
therefore attractive but challenging targets for drug design. One of the challenges in …