ScanNet: an interpretable geometric deep learning model for structure-based protein binding site prediction

J Tubiana, D Schneidman-Duhovny, HJ Wolfson - Nature Methods, 2022 - nature.com
Predicting the functional sites of a protein from its structure, such as the binding sites of small
molecules, other proteins or antibodies, sheds light on its function in vivo. Currently, two …

Simple mechanisms for the evolution of protein complexity

AS Pillai, GKA Hochberg, JW Thornton - Protein science, 2022 - Wiley Online Library
Proteins are tiny models of biological complexity: specific interactions among their many
amino acids cause proteins to fold into elaborate structures, assemble with other proteins …

[HTML][HTML] How gene duplication diversifies the landscape of protein oligomeric state and function

S Mallik, DS Tawfik, ED Levy - Current opinion in genetics & development, 2022 - Elsevier
Oligomeric proteins are central to cellular life and the duplication and divergence of their
genes is a key driver of evolutionary innovations. The duplication of a gene coding for an …

[HTML][HTML] An atlas of protein homo-oligomerization across domains of life

H Schweke, M Pacesa, T Levin, CA Goverde, P Kumar… - Cell, 2024 - cell.com
Protein structures are essential to understanding cellular processes in molecular detail.
While advances in artificial intelligence revealed the tertiary structure of proteins at scale …

Structural plasticity enables evolution and innovation of RuBisCO assemblies

AK Liu, JH Pereira, AJ Kehl, DJ Rosenberg, DJ Orr… - Science …, 2022 - science.org
Oligomerization is a core structural feature that defines the form and function of many
proteins. Most proteins form molecular complexes; however, there remains a dearth of …

Manipulating interfaces of electrocatalysts down to atomic scales: fundamentals, strategies, and electrocatalytic applications

X Li, Z Kou, J Wang - Small Methods, 2021 - Wiley Online Library
Raising electrocatalysis by rationally devising catalysts plays a core role in almost all
renewable energy conversion and storage systems. The principal catalytic properties can be …

A complete rule set for designing symmetry combination materials from protein molecules

J Laniado, TO Yeates - Proceedings of the National …, 2020 - National Acad Sciences
Diverse efforts in protein engineering are beginning to produce novel kinds of symmetric self-
assembling architectures, from protein cages to extended two-dimensional (2D) and three …

Protein quaternary structures in solution are a mixture of multiple forms

S Marciano, D Dey, D Listov, SJ Fleishman… - Chemical …, 2022 - pubs.rsc.org
Over half the proteins in the E. coli cytoplasm form homo or hetero-oligomeric structures.
Experimentally determined structures are often considered in determining a protein's …

Frequent transitions in self-assembly across the evolution of a central metabolic enzyme

FL Sendker, T Schlotthauer, CN Mais, YK Lo… - Nature …, 2024 - nature.com
Many enzymes assemble into homomeric protein complexes comprising multiple copies of
one protein. Because structural form is usually assumed to follow function in biochemistry …

Automated evaluation of quaternary structures from protein crystals

S Bliven, A Lafita, A Parker, G Capitani… - PLoS computational …, 2018 - journals.plos.org
A correct assessment of the quaternary structure of proteins is a fundamental prerequisite to
understanding their function, physico-chemical properties and mode of interaction with other …