[HTML][HTML] Recent advances in rational approaches for enzyme engineering

K Steiner, H Schwab - Computational and structural biotechnology journal, 2012 - Elsevier
Enzymes are an attractive alternative in the asymmetric syntheses of chiral building blocks.
To meet the requirements of industrial biotechnology and to introduce new functionalities …

Biomolecular engineering for nanobio/bionanotechnology

T Nagamune - Nano convergence, 2017 - Springer
Biomolecular engineering can be used to purposefully manipulate biomolecules, such as
peptides, proteins, nucleic acids and lipids, within the framework of the relations among their …

Deep geometric representations for modeling effects of mutations on protein-protein binding affinity

X Liu, Y Luo, P Li, S Song, J Peng - PLoS computational biology, 2021 - journals.plos.org
Modeling the impact of amino acid mutations on protein-protein interaction plays a crucial
role in protein engineering and drug design. In this study, we develop GeoPPI, a novel …

Current trends in asymmetric synthesis with aldolases

P Clapes, X Garrabou - Advanced Synthesis & Catalysis, 2011 - Wiley Online Library
Biocatalytic carbon‐carbon bond formation by means of aldolases offers an exceptionally
stereoselective and green tool for this strategic reaction in synthetic organic chemistry …

Computational design tools for synthetic biology

MA Marchisio, J Stelling - Current opinion in biotechnology, 2009 - Elsevier
Computer-aided design, pervasive in other engineering disciplines, is currently developing
in synthetic biology. Concepts for standardization and hierarchies of parts, devices and …

Rise and demise of bioinformatics? Promise and progress

CA Ouzounis - PLoS computational biology, 2012 - journals.plos.org
The field of bioinformatics and computational biology has gone through a number of
transformations during the past 15 years, establishing itself as a key component of new …

Energy functions in de novo protein design: current challenges and future prospects

Z Li, Y Yang, J Zhan, L Dai… - Annual review of …, 2013 - annualreviews.org
In the past decade, a concerted effort to successfully capture specific tertiary packing
interactions produced specific three-dimensional structures for many de novo designed …

Direct prediction of profiles of sequences compatible with a protein structure by neural networks with fragment‐based local and energy‐based nonlocal profiles

Z Li, Y Yang, E Faraggi, J Zhan… - … : Structure, Function, and …, 2014 - Wiley Online Library
Locating sequences compatible with a protein structural fold is the well‐known inverse
protein‐folding problem. While significant progress has been made, the success rate of …

Origins of catalysis by computationally designed retroaldolase enzymes

JK Lassila, D Baker… - Proceedings of the …, 2010 - National Acad Sciences
We have investigated recently reported computationally designed retroaldolase enzymes
with the goal of understanding the extent and the origins of their catalytic power. Direct …

[HTML][HTML] Computer-aided protein directed evolution: a review of web servers, databases and other computational tools for protein engineering

R Verma, U Schwaneberg, D Roccatano - Computational and structural …, 2012 - Elsevier
The combination of computational and directed evolution methods has proven a winning
strategy for protein engineering. We refer to this approach as computer-aided protein …