[HTML][HTML] Integrative structural biology in the era of accurate structure prediction

G Masrati, M Landau, N Ben-Tal, A Lupas… - Journal of molecular …, 2021 - Elsevier
Characterizing the three-dimensional structure of macromolecules is central to
understanding their function. Traditionally, structures of proteins and their complexes have …

Expanding the versatility of natural and de novo designed coiled coils and helical bundles

M ElGamacy, BH Alvarez - Current Opinion in Structural Biology, 2021 - Elsevier
Natural helical bundles (HBs) constitute a ubiquitous class of protein folds built of two or
more longitudinally arranged α-helices. They adopt topologies that include symmetric, highly …

A topological refactoring design strategy yields highly stable granulopoietic proteins

J Skokowa, B Hernandez Alvarez, M Coles… - Nature …, 2022 - nature.com
Protein therapeutics frequently face major challenges, including complicated production,
instability, poor solubility, and aggregation. De novo protein design can readily address …

The design of functional proteins using tensorized energy calculations

K Maksymenko, A Maurer, N Aghaallaei, C Barry… - Cell Reports …, 2023 - cell.com
In protein design, the energy associated with a huge number of sequence-conformer
perturbations has to be routinely estimated. Hence, enhancing the throughput and accuracy …

Computational design of intrinsically disordered protein regions by matching bulk molecular properties

B Strome, K Elemam, I Pritisanac, JD Forman-Kay… - bioRxiv, 2023 - biorxiv.org
Algorithms for computational protein design usually begin with a 3D structure and design an
amino acid sequence that will fold into that structure. Since intrinsically disordered protein …

The Damietta Server: a comprehensive protein design toolkit

I Grin, K Maksymenko, T Wörtwein… - Nucleic Acids …, 2024 - academic.oup.com
The growing importance of protein design to various research disciplines motivates the
development of integrative computational platforms that enhance the accessibility and …

Tuning of granulopoietic signaling by de novo designed agonists

T Ullrich, C Pollmann, M Ritter, J Haaf, N Aghaallaei… - bioRxiv, 2023 - biorxiv.org
Enhancing the efficacy of cytokine-based therapies by systematically tuning how an agonist
associates its receptor is emerging as a powerful new concept in drug discovery. De novo …

Integrated autolysis, DNA hydrolysis and precipitation enables an improved bioprocess for Q-Griffithsin, a broad-spectrum antiviral and clinical-stage anti-COVID-19 …

JS Decker, R Menacho-Melgar, MD Lynch - Biochemical Engineering …, 2022 - Elsevier
Across the biomanufacturing industry, innovations are needed to improve efficiency and
flexibility, especially in the face of challenges such as the COVID-19 pandemic. Here we …

Accelerating therapeutic protein design

M ElGamacy - Advances in Protein Chemistry and Structural Biology, 2022 - Elsevier
Protein structures provide for defined microenvironments that can support complex
pharmacological functions, otherwise unachievable by small molecules. The advent of …

[PDF][PDF] Advancements in Low-Cost, non-Conventional Bioprocessing Methods for Therapeutic Proteins

JS Decker - 2022 - dukespace.lib.duke.edu
Protein-based drugs are becoming increasingly important both therapeutically and
economically. However, these drugs are complex and costly to manufacture, making them …