Recent progress in the synthesis of advanced biofuel and bioproducts

BF Pfleger, R Takors - Current Opinion in Biotechnology, 2023 - Elsevier
Highlights●Why biofuels and bioproducts remain critical to society●What molecular
products can be made by biotechnology using available feedstocks●How new systems and …

Insertions and deletions (indels): a missing piece of the protein engineering jigsaw

CM Miton, N Tokuriki - Biochemistry, 2022 - ACS Publications
Over the years, protein engineers have studied nature and borrowed its tricks to accelerate
protein evolution in the test tube. While there have been considerable advances, our ability …

Learning epistasis and residue coevolution patterns: Current trends and future perspectives for advancing enzyme engineering

M Wittmund, F Cadet, MD Davari - ACS catalysis, 2022 - ACS Publications
Engineering proteins and enzymes with the desired functionality has broad applications in
molecular biology, biotechnology, biomedical sciences, health, and medicine. The vastness …

Computational biophysical characterization of the SARS-CoV-2 spike protein binding with the ACE2 receptor and implications for infectivity

R Chowdhury, VS Boorla, CD Maranas - Computational and structural …, 2020 - Elsevier
SARS-CoV-2 is a novel highly virulent pathogen which gains entry to human cells by
binding with the cell surface receptor–angiotensin converting enzyme (ACE2). We …

Towards an optimal monoclonal antibody with higher binding affinity to the receptor-binding domain of SARS-CoV-2 spike proteins from different variants

A Neamtu, F Mocci, A Laaksonen… - Colloids and Surfaces B …, 2023 - Elsevier
A highly efficient and robust multiple scales in silico protocol, consisting of atomistic
Molecular Dynamics (MD), coarse-grain (CG) MD, and constant-pH CG Monte Carlo (MC) …

Computational approaches for enteric methane mitigation research: from fermi calculations to artificial intelligence paradigms

R Chowdhury, AN Frazier, JA Koziel… - Animal …, 2024 - academic.oup.com
Background Governments worldwide have made various commitments to address climate
change. The first international treaty related to climate change was the Kyoto Protocol of the …

Compendious survey of protein tandem repeats in inbred mouse strains

A Arslan - BMC Genomic Data, 2022 - Springer
Short tandem repeats (STRs) play a crucial role in genetic diseases. However, classic
disease models such as inbred mice lack such genome wide data in public domain. The …

Engineering sensitivity and specificity of AraC-based biosensors responsive to triacetic acid lactone and orsellinic acid

Z Wang, A Doshi, R Chowdhury, Y Wang… - Protein Engineering …, 2020 - academic.oup.com
We previously described the design of triacetic acid lactone (TAL) biosensor 'AraC-TAL1',
based on the AraC regulatory protein. Although useful as a tool to screen for enhanced TAL …

[HTML][HTML] Enzyme structure correlates with variant effect predictability

F van der Flier, D Estell, S Pricelius… - Computational and …, 2024 - Elsevier
Protein engineering increasingly relies on machine learning models to computationally pre-
screen promising novel candidates. Although machine learning approaches have proven …

Improved Functional Classification of Hydrolases through Pairwise Structural Similarity of Reaction Cores

S Ferdous, P Gupta, YC Teoh, KA Sajeevan, K Hainlin… - bioRxiv, 2025 - biorxiv.org
We report a systematic pipeline is for extracting the catalytically relevant reactive site in
addition to the surrounding allosterically linked residue shells around the reaction site of the …