Exploring protein functions from structural flexibility using CABS‐flex modeling

C Nithin, RP Fornari, SP Pilla, K Wroblewski… - Protein …, 2024 - Wiley Online Library
Understanding protein function often necessitates characterizing the flexibility of protein
structures. However, simulating protein flexibility poses significant challenges due to the …

Aggrescan4D: A comprehensive tool for pH‐dependent analysis and engineering of protein aggregation propensity

M Zalewski, V Iglesias, O Bárcenas, S Ventura… - Protein …, 2024 - Wiley Online Library
Abstract Aggrescan4D (A4D) is an advanced computational tool designed for predicting
protein aggregation, leveraging structural information and the influence of pH. Building upon …

Aggrescan4D: structure-informed analysis of pH-dependent protein aggregation

O Bárcenas, A Kuriata, M Zalewski… - Nucleic Acids …, 2024 - academic.oup.com
Protein aggregation is behind the genesis of incurable diseases and imposes constraints on
drug discovery and the industrial production and formulation of proteins. Over the years, we …

From experimental studies to computational approaches: recent trends in designing novel therapeutics for amyloidogenesis

P Ghosh, A Kundu, D Ganguly - Journal of Materials Chemistry B, 2025 - pubs.rsc.org
Amyloidosis is a condition marked by misfolded proteins that build up in tissues and
eventually destroy organs. It has been connected to a number of fatal illnesses, including …

Machine learning for predicting protein properties: A comprehensive review

Y Wang, Y Zhang, X Zhan, Y He, Y Yang, L Cheng… - Neurocomputing, 2024 - Elsevier
In the field of protein engineering, the function and structure of proteins are key to
understanding cellular mechanisms, biological evolution, and biodiversity. With the …

[HTML][HTML] Bioengineered self-assembled nanofibrils for high-affinity SARS-CoV-2 capture and neutralization

M Behbahanipour, S Navarro, O Bárcenas… - Journal of colloid and …, 2024 - Elsevier
The recent coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute
respiratory syndrome coronavirus 2 (SARS-CoV-2) has spurred intense research efforts to …

[HTML][HTML] Aggregating amyloid resources: A comprehensive review of databases on amyloid-like aggregation

V Iglesias, J Chilimoniuk, C Pintado-Grima… - Computational and …, 2024 - Elsevier
Protein aggregation is responsible for several degenerative conditions in humans, and it is
also a bottleneck in industrial protein production and storage of biotherapeutics …

[HTML][HTML] Comparative modeling reveals the molecular determinants of aneuploidy fitness cost in a wild yeast model

J Rojas, J Hose, HA Dutcher, M Place, JF Wolters… - bioRxiv, 2024 - ncbi.nlm.nih.gov
Although implicated as deleterious in many organisms, aneuploidy can underlie rapid
phenotypic evolution. However, aneuploidy will only be maintained if the benefit outweighs …