Computational approaches to therapeutic antibody design: established methods and emerging trends

RA Norman, F Ambrosetti, AMJJ Bonvin… - Briefings in …, 2020 - academic.oup.com
Antibodies are proteins that recognize the molecular surfaces of potentially noxious
molecules to mount an adaptive immune response or, in the case of autoimmune diseases …

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 …

COVID-19 spike-host cell receptor GRP78 binding site prediction

IM Ibrahim, DH Abdelmalek, ME Elshahat, AA Elfiky - Journal of infection, 2020 - Elsevier
Objectives Understanding the novel coronavirus (COVID-19) mode of host cell recognition
may help to fight the disease and save lives. The spike protein of coronaviruses is the main …

HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy

Y Yan, D Zhang, P Zhou, B Li… - Nucleic acids research, 2017 - academic.oup.com
Protein–protein and protein–DNA/RNA interactions play a fundamental role in a variety of
biological processes. Determining the complex structures of these interactions is valuable, in …

[HTML][HTML] The HADDOCK2. 2 web server: user-friendly integrative modeling of biomolecular complexes

GCP Van Zundert, J Rodrigues, M Trellet… - Journal of molecular …, 2016 - Elsevier
The prediction of the quaternary structure of biomolecular macromolecules is of paramount
importance for fundamental understanding of cellular processes and drug design. In the era …

In situ structural analysis of the human nuclear pore complex

A Von Appen, J Kosinski, L Sparks, A Ori, AL DiGuilio… - Nature, 2015 - nature.com
Nuclear pore complexes are fundamental components of all eukaryotic cells that mediate
nucleocytoplasmic exchange. Determining their 110-megadalton structure imposes a …

Sequence co-evolution gives 3D contacts and structures of protein complexes

TA Hopf, CPI Schärfe, JP Rodrigues, AG Green… - elife, 2014 - elifesciences.org
Protein–protein interactions are fundamental to many biological processes. Experimental
screens have identified tens of thousands of interactions, and structural biology has …

The HADDOCK web server for data-driven biomolecular docking

SJ De Vries, M Van Dijk, AMJJ Bonvin - Nature protocols, 2010 - nature.com
Computational docking is the prediction or modeling of the three-dimensional structure of a
biomolecular complex, starting from the structures of the individual molecules in their free …

A deep learning framework for modeling structural features of RNA-binding protein targets

S Zhang, J Zhou, H Hu, H Gong, L Chen… - Nucleic acids …, 2016 - academic.oup.com
RNA-binding proteins (RBPs) play important roles in the post-transcriptional control of
RNAs. Identifying RBP binding sites and characterizing RBP binding preferences are key …

Mechanism of activation of protein kinase JAK2 by the growth hormone receptor

AJ Brooks, W Dai, ML O'Mara, D Abankwa, Y Chhabra… - Science, 2014 - science.org
Introduction Class I cytokines regulate key processes such as growth, lactation,
hematopoiesis, and immune function and contribute to oncogenesis. Although the …