Utility of B-factors in protein science: interpreting rigidity, flexibility, and internal motion and engineering thermostability

Z Sun, Q Liu, G Qu, Y Feng, MT Reetz - Chemical reviews, 2019 - ACS Publications
The term B-factor, sometimes called the Debye–Waller factor, temperature factor, or atomic
displacement parameter, is used in protein crystallography to describe the attenuation of X …

ATSE: a peptide toxicity predictor by exploiting structural and evolutionary information based on graph neural network and attention mechanism

L Wei, X Ye, Y Xue, T Sakurai… - Briefings in Bioinformatics, 2021 - academic.oup.com
Motivation: Peptides have recently emerged as promising therapeutic agents against
various diseases. For both research and safety regulation purposes, it is of high importance …

[HTML][HTML] The role and future prospects of artificial intelligence algorithms in peptide drug development

Z Chen, R Wang, J Guo, X Wang - Biomedicine & Pharmacotherapy, 2024 - Elsevier
Peptide medications have been more well-known in recent years due to their many benefits,
including low side effects, high biological activity, specificity, effectiveness, and so on. Over …

Two zinc-binding domains in the transporter AdcA from Streptococcus pyogenes facilitate high-affinity binding and fast transport of zinc

K Cao, N Li, H Wang, X Cao, J He, B Zhang… - Journal of Biological …, 2018 - ASBMB
Zinc is an essential metal in bacteria. One important bacterial zinc transporter is AdcA, and
most bacteria possess AdcA homologs that are single-domain small proteins due to better …

The structure of protein dynamic space

S Rackovsky, HA Scheraga - Proceedings of the National …, 2020 - National Acad Sciences
We use a bioinformatic description of amino acid dynamic properties, based on residue-
specific average B factors, to construct a dynamics-based, large-scale description of a space …

Enzyme Substrate Prediction from Three-Dimensional Feature Representations Using Space-Filling Curves

D Rappoport, A Jinich - Journal of chemical information and …, 2023 - ACS Publications
Compact and interpretable structural feature representations are required for accurately
predicting properties and function of proteins. In this work, we construct and evaluate three …

TGC-ARG: Anticipating Antibiotic Resistance via Transformer-Based Modeling and Contrastive Learning

Y Dong, H Quan, C Ma, L Shan, L Deng - International Journal of …, 2024 - mdpi.com
In various domains, including everyday activities, agricultural practices, and medical
treatments, the escalating challenge of antibiotic resistance poses a significant concern …

Identification of Two Flip-Over Genes in Grass Family as Potential Signature of C4 Photosynthesis Evolution

C Wu, D Guo - International Journal of Molecular Sciences, 2023 - mdpi.com
In flowering plants, C4 photosynthesis is superior to C3 type in carbon fixation efficiency and
adaptation to extreme environmental conditions, but the mechanisms behind the assembly …

Exploring computational tools for improved structural design and stability of helical AApeptides

T Li, S Song, Y He - Supramolecular Materials, 2023 - Elsevier
Peptidomimetics have garnered increased attention due to their unique structural properties
and self-assembly, as well as their promising applications in material sciences and …

In search of a dynamical vocabulary: a pipeline to construct a basis of shared traits in large-scale motions of proteins

T Tarenzi, G Mattiotti, M Rigoli, R Potestio - Applied Sciences, 2022 - mdpi.com
The paradigmatic sequence–structure–dynamics–function relation in proteins is currently
well established in the scientific community; in particular, a large effort has been made to …