Development of small molecules designed to modulate protein–protein interactions

Y Che, BR Brooks, GR Marshall - Journal of computer-aided molecular …, 2006 - Springer
Protein–protein interactions are ubiquitous, essential to almost all known biological
processes, and offer attractive opportunities for therapeutic intervention. Developing small …

Principles and pitfalls in designing site‐directed peptide ligands

AB Edmundson, DL Harris, ZC Fan… - Proteins: Structure …, 1993 - Wiley Online Library
An immunoglobulin light chain dimer with a large generic binding cavity was used as a host
molecule for designing a series of peptide guest ligands. In a screening procedure peptides …

Examination of shape complementarity in docking of Unbound proteins

R Norel, D Petrey, HJ Wolfson… - … : Structure, Function, and …, 1999 - Wiley Online Library
Here we carry out an examination of shape complementarity as a criterion in protein‐protein
docking and binding. Specifically, we examine the quality of shape complementarity as a …

Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons

A Nicholls, KA Sharp, B Honig - Proteins: Structure, Function …, 1991 - Wiley Online Library
We demonstrate in this work that the surface tension, water‐organic solvent, transfer‐free
energies and the thermodynamics of melting of linear alkanes provide fundamental insights …

Sampling and energy evaluation challenges in ligand binding protein design

J Dou, L Doyle, P Jr Greisen, A Schena, H Park… - Protein …, 2017 - Wiley Online Library
The steroid hormone 17α‐hydroxylprogesterone (17‐OHP) is a biomarker for congenital
adrenal hyperplasia and hence there is considerable interest in development of sensors for …

Structural motifs at protein‐protein interfaces: Protein cores versus two‐state and three‐state model complexes

CJ Tsai, D Xu, R Nussinov - Protein Science, 1997 - Wiley Online Library
The general similarity in the forces governing protein folding and protein-protein
associations has led us to examine the similarity in the architectural motifs between the …

Studies of protein‐protein interfaces: a statistical analysis of the hydrophobic effect

CJ Tsai, SL Lin, HJ Wolfson, R Nussinov - Protein Science, 1997 - Wiley Online Library
Data sets of 362 structurally nonredundant protein‐protein interfaces and of 57 symmetry‐
related oligomeric interfaces have been used to explore whether the hydrophobic effect that …

Designed protein-protein association

D Grueninger, N Treiber, MOP Ziegler, JWA Koetter… - Science, 2008 - science.org
The analysis of natural contact interfaces between protein subunits and between proteins
has disclosed some general rules governing their association. We have applied these rules …

[HTML][HTML] Emerging themes in the computational design of novel enzymes and protein–protein interfaces

SD Khare, SJ Fleishman - FEBS letters, 2013 - Elsevier
Recent years have seen the first applications of computational protein design to generate
novel catalysts, binding pairs of proteins, protein inhibitors, and large oligomeric assemblies …

Blind predictions of protein interfaces by docking calculations in CAPRI

MF Lensink, SJ Wodak - Proteins: Structure, Function, and …, 2010 - Wiley Online Library
Reliable prediction of the amino acid residues involved in protein–protein interfaces can
provide valuable insight into protein function, and inform mutagenesis studies, and drug …