Paleoproteomics

C Warinner, K Korzow Richter, MJ Collins - Chemical reviews, 2022 - ACS Publications
Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of
molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics …

Using machine learning to predict the effects and consequences of mutations in proteins

DJ Diaz, AV Kulikova, AD Ellington, CO Wilke - Current opinion in structural …, 2023 - Elsevier
Abstract Machine and deep learning approaches can leverage the increasingly available
massive datasets of protein sequences, structures, and mutational effects to predict variants …

Biological soft matter: intrinsically disordered proteins in liquid–liquid phase separation and biomolecular condensates

AV Fonin, IA Antifeeva, IM Kuznetsova… - Essays in …, 2022 - portlandpress.com
The facts that many proteins with crucial biological functions do not have unique structures
and that many biological processes are compartmentalized into the liquid-like biomolecular …

Quantitative mass spectrometry imaging: therapeutics & biomolecules

JH Holbrook, GE Kemper, AB Hummon - Chemical Communications, 2024 - pubs.rsc.org
Mass spectrometry imaging (MSI) has become increasingly utilized in the analysis of
biological molecules. MSI grants the ability to spatially map thousands of molecules within …

Genomic characterization and virulence gene profiling of Erysipelothrix rhusiopathiae isolated from widespread muskox mortalities in the Canadian Arctic …

LV Seru, TL Forde, A Roberto-Charron, F Mavrot… - BMC genomics, 2024 - Springer
Background Muskoxen are important ecosystem components and provide food, economic
opportunities, and cultural well-being for Indigenous communities in the Canadian Arctic …

Deep learning for flexible and site-specific protein docking and design

M McPartlon, J Xu - BioRxiv, 2023 - biorxiv.org
Protein complexes are vital to many biological processes and their understanding can lead
to the development of new drugs and therapies. Although the structure of individual protein …

Explainablefold: Understanding alphafold prediction with explainable ai

J Tan, Y Zhang - Proceedings of the 29th ACM SIGKDD Conference on …, 2023 - dl.acm.org
This paper presents ExplainableFold (xFold), which is an Explainable AI framework for
protein structure prediction. Despite the success of AI-based methods such as AlphaFold …

Two sequence-and two structure-based ML models have learned different aspects of protein biochemistry

AV Kulikova, DJ Diaz, T Chen, TJ Cole, AD Ellington… - Scientific Reports, 2023 - nature.com
Deep learning models are seeing increased use as methods to predict mutational effects or
allowed mutations in proteins. The models commonly used for these purposes include large …

Interaction between polydopamine-based IONPs and human serum albumin (HSA): a spectroscopic analysis with cytotoxicity impact

H Shekhar, P Behera, A Naik, M Mishra, H Sahoo - Nanotoxicology, 2024 - Taylor & Francis
Iron oxide nanoparticles (IONPs) have been extensively explored in biomedicine, bio-
sensing, hyperthermia, and drug/gene delivery, attributed to their versatile and tunable …

Inhibition mechanism study for diallyl thiosulfinate (allicin) against crucial bacterial proteins through in silico molecular docking simulation

S Bhattacharya, D Sen, C Bhattacharjee - Process Biochemistry, 2022 - Elsevier
The present investigation illustrates the in silico structure based drug design method to
identify the target bacterial proteins of diallyl thiosulfinate (allicin) and its inhibitory mode of …