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 …
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
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 …
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 …
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 …
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?
Protein-protein interactions (PPIs) are ubiquitous biomolecular processes that are central to
virtually all aspects of cellular function. Identifying small molecules that modulate specific …
virtually all aspects of cellular function. Identifying small molecules that modulate specific …
In silico structure-based approaches to discover protein-protein interaction-targeting drugs
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 …
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 …
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 …
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
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 …
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 …
therefore attractive but challenging targets for drug design. One of the challenges in …