Assessment of the CASP14 assembly predictions

B Ozden, A Kryshtafovych… - … : Structure, Function, and …, 2021 - Wiley Online Library
In CASP14, 39 research groups submitted more than 2500 3D models on 22 protein
complexes. In general, the community performed well in predicting the fold of the assemblies …

SymProFold: Structural prediction of symmetrical biological assemblies

C Buhlheller, T Sagmeister, C Grininger… - Nature …, 2024 - nature.com
Symmetry in nature often emerges from self-assembly processes and serves a wide range of
functions. Cell surface layers (S-layers) form symmetrical lattices on many bacterial and …

HIV-1 VRC01 germline-targeting immunogens select distinct epitope-specific B cell receptors

YR Lin, KR Parks, C Weidle, AS Naidu, A Khechaduri… - Immunity, 2020 - cell.com
Activating precursor B cell receptors of HIV-1 broadly neutralizing antibodies requires
specifically designed immunogens. Here, we compared the abilities of three such germline …

Large protein complex interfaces have evolved to promote cotranslational assembly

M Badonyi, JA Marsh - Elife, 2022 - elifesciences.org
Assembly pathways of protein complexes should be precise and efficient to minimise
misfolding and unwanted interactions with other proteins in the cell. One way to achieve this …

Domain-based protein docking with extremely large conformational changes

C Christoffer, D Kihara - Journal of molecular biology, 2022 - Elsevier
Proteins are key components in many processes in living cells, and physical interactions
with other proteins and nucleic acids often form key parts of their functions. In many cases …

Analytical symmetry detection in protein assemblies. I. Cyclic symmetries

G Pagès, E Kinzina, S Grudinin - Journal of Structural Biology, 2018 - Elsevier
Symmetry in protein, and, more generally, in macromolecular assemblies is a key point to
understand their structure, stability and function. Many symmetrical assemblies are currently …

Detection of rotational symmetry in curves represented by the slope chain code

W Aguilar, M Alvarado-Gonzalez, E Garduno… - Pattern Recognition, 2020 - Elsevier
We present a new approach based on the Slope Chain Code to determine whether a curve
is rotational symmetrical and its order of symmetry. The proposed approach works for open …

Coarse grained molecular dynamic simulations for the study of TNF receptor family members' transmembrane organization

MP Sica, CR Smulski - Frontiers in Cell and Developmental Biology, 2021 - frontiersin.org
The Tumor Necrosis Factor (TNF) and the TNF receptor (TNFR) superfamilies are composed
of 19 ligands and 30 receptors, respectively. The oligomeric properties of ligands, both …

[HTML][HTML] MemSTATS: a benchmark set of membrane protein symmetries and pseudosymmetries

AA Aleksandrova, E Sarti, LR Forrest - Journal of molecular biology, 2020 - Elsevier
In membrane proteins, symmetry and pseudosymmetry often have functional or evolutionary
implications. However, available symmetry detection methods have not been tested …

Side chain flexibility and the symmetry of protein homodimers

Y Shalit, I Tuvi-Arad - PLoS One, 2020 - journals.plos.org
A comprehensive analysis of crystallographic data of 565 high-resolution protein
homodimers comprised of over 250,000 residues suggests that amino acids form two groups …