Computational prediction of protein–protein binding affinities
T Siebenmorgen, M Zacharias - Wiley Interdisciplinary Reviews …, 2020 - Wiley Online Library
Protein–protein interactions form central elements of almost all cellular processes.
Knowledge of the structure of protein–protein complexes but also of the binding affinity is of …
Knowledge of the structure of protein–protein complexes but also of the binding affinity is of …
Binding affinity prediction with different force fields: examination of the linear interaction energy method
M Almlöf, BØO Brandsdal… - Journal of computational …, 2004 - Wiley Online Library
A systematic study of the linear interaction energy (LIE) method and the possible
dependence of its parameterization on the force field and system (receptor binding site) is …
dependence of its parameterization on the force field and system (receptor binding site) is …
Protein–protein interactions: scoring schemes and binding affinity
MM Gromiha, K Yugandhar, S Jemimah - Current opinion in structural …, 2017 - Elsevier
Highlights•Reviewed scoring schemes and conformational sampling for protein–protein
complex structure prediction.•Discussed the database for binding affinity of complexes and …
complex structure prediction.•Discussed the database for binding affinity of complexes and …
[HTML][HTML] Deciphering protein–protein interactions. Part II. Computational methods to predict protein and domain interaction partners
BA Shoemaker, AR Panchenko - PLoS computational biology, 2007 - journals.plos.org
Recent advances in high-throughput experimental methods for the identification of protein
interactions have resulted in a large amount of diverse data that are somewhat incomplete …
interactions have resulted in a large amount of diverse data that are somewhat incomplete …
Prediction of physical protein–protein interactions
A Szilagyi, V Grimm, AK Arakaki, J Skolnick - Physical biology, 2005 - iopscience.iop.org
Many essential cellular processes such as signal transduction, transport, cellular motion and
most regulatory mechanisms are mediated by protein–protein interactions. In recent years …
most regulatory mechanisms are mediated by protein–protein interactions. In recent years …
PRODIGY: a web server for predicting the binding affinity of protein–protein complexes
Gaining insights into the structural determinants of protein–protein interactions holds the key
for a deeper understanding of biological functions, diseases and development of …
for a deeper understanding of biological functions, diseases and development of …
Prediction of protein–protein binding free energies
We present an energy function for predicting binding free energies of protein–protein
complexes, using the three‐dimensional structures of the complex and unbound proteins as …
complexes, using the three‐dimensional structures of the complex and unbound proteins as …
Molecular mechanics methods for predicting protein–ligand binding
N Huang, C Kalyanaraman, K Bernacki… - Physical Chemistry …, 2006 - pubs.rsc.org
Ligand binding affinity prediction is one of the most important applications of computational
chemistry. However, accurately ranking compounds with respect to their estimated binding …
chemistry. However, accurately ranking compounds with respect to their estimated binding …
Evaluation of predicted protein–protein complexes by binding free energy simulations
T Siebenmorgen, M Zacharias - Journal of chemical theory and …, 2019 - ACS Publications
The accurate prediction of protein–protein complex geometries is of major importance to
ultimately model the complete interactome of interacting proteins in a cell. A major …
ultimately model the complete interactome of interacting proteins in a cell. A major …
A structure‐based benchmark for protein–protein binding affinity
We have assembled a nonredundant set of 144 protein–protein complexes that have high‐
resolution structures available for both the complexes and their unbound components, and …
resolution structures available for both the complexes and their unbound components, and …