What method to use for protein–protein docking?
Highlights•The best servers based on “free” docking methods find acceptable models
among the top 10 predictions for around 40% of the targets.•Re-ranking the predictions by a …
among the top 10 predictions for around 40% of the targets.•Re-ranking the predictions by a …
[HTML][HTML] Affinity maturation of antibody fragments: A review encompassing the development from random approaches to computational rational optimization
J Li, G Kang, J Wang, H Yuan, Y Wu, S Meng… - International journal of …, 2023 - Elsevier
Routinely screened antibody fragments usually require further in vitro maturation to achieve
the desired biophysical properties. Blind in vitro strategies can produce improved ligands by …
the desired biophysical properties. Blind in vitro strategies can produce improved ligands by …
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 …
Contacts-based prediction of binding affinity in protein–protein complexes
A Vangone, AMJJ Bonvin - elife, 2015 - elifesciences.org
Almost all critical functions in cells rely on specific protein–protein interactions.
Understanding these is therefore crucial in the investigation of biological systems. Despite …
Understanding these is therefore crucial in the investigation of biological systems. Despite …
Updates to the integrated protein–protein interaction benchmarks: docking benchmark version 5 and affinity benchmark version 2
We present an updated and integrated version of our widely used protein–protein docking
and binding affinity benchmarks. The benchmarks consist of non-redundant, high-quality …
and binding affinity benchmarks. The benchmarks consist of non-redundant, high-quality …
SKEMPI 2.0: an updated benchmark of changes in protein–protein binding energy, kinetics and thermodynamics upon mutation
J Jankauskaitė, B Jiménez-García, J Dapkūnas… - …, 2019 - academic.oup.com
Motivation Understanding the relationship between the sequence, structure, binding energy,
binding kinetics and binding thermodynamics of protein–protein interactions is crucial to …
binding kinetics and binding thermodynamics of protein–protein interactions is crucial to …
Classification and prediction of protein–protein interaction interface using machine learning algorithm
S Das, S Chakrabarti - Scientific reports, 2021 - nature.com
Structural insight of the protein–protein interaction (PPI) interface can provide knowledge
about the kinetics, thermodynamics and molecular functions of the complex while …
about the kinetics, thermodynamics and molecular functions of the complex while …
Unsupervised protein-ligand binding energy prediction via neural euler's rotation equation
Protein-ligand binding prediction is a fundamental problem in AI-driven drug discovery.
Previous work focused on supervised learning methods for small molecules where binding …
Previous work focused on supervised learning methods for small molecules where binding …
An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants
Accurate predictive modeling of antibody-antigen complex structures and structure-based
antibody design remain major challenges in computational biology, with implications for …
antibody design remain major challenges in computational biology, with implications for …
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 …