Engineering protein fragments via evolutionary and protein–protein interaction algorithms: de novo design of peptide inhibitors for FOF1‐ATP synthase
Sign Up to like & getrecommendations! Published in 2020 at "FEBS Letters"
DOI: 10.1002/1873-3468.13988
Abstract: Enzyme subunit interfaces have remarkable potential in drug design as both target and scaffold for their own inhibitors. We show an evolution‐driven strategy for the de novo design of peptide inhibitors targeting interfaces of the… read more here.
Keywords: protein; atp synthase; peptide; novo design ... See more keywords
Learning from Nature: From a Marine Natural Product to Synthetic Cyclooxygenase‐1 Inhibitors by Automated De Novo Design
Sign Up to like & getrecommendations! Published in 2021 at "Advanced Science"
DOI: 10.1002/advs.202100832
Abstract: Abstract The repertoire of natural products offers tremendous opportunities for chemical biology and drug discovery. Natural product‐inspired synthetic molecules represent an ecologically and economically sustainable alternative to the direct utilization of natural products. De novo… read more here.
Keywords: design; natural products; natural product; novo design ... See more keywords
Customizable de novo design strategies for DOCK: Application to HIVgp41 and other therapeutic targets
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.25052
Abstract: De novo design can be used to explore vast areas of chemical space in computational lead discovery. As a complement to virtual screening, from‐scratch construction of molecules is not limited to compounds in pre‐existing vendor… read more here.
Keywords: design strategies; customizable novo; dock application; novo design ... See more keywords
Deep generative models for ligand‐based de novo design applied to multi‐parametric optimization
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.26826
Abstract: Multi‐parameter optimization (MPO) is a major challenge in new chemical entity (NCE) drug discovery. Recently, promising results were reported for deep learning generative models applied to de novo molecular design, but, to our knowledge, until… read more here.
Keywords: generative models; optimization; based novo; novo design ... See more keywords
A Pareto Algorithm for Efficient De Novo Design of Multi‐functional Molecules
Sign Up to like & getrecommendations! Published in 2017 at "Molecular Informatics"
DOI: 10.1002/minf.201600044
Abstract: We have introduced a Pareto sorting algorithm into Synopsis, a de novo design program that generates synthesizable molecules with desirable properties. We give a detailed description of the algorithm and illustrate its working in 2… read more here.
Keywords: efficient novo; novo design; design multi; pareto algorithm ... See more keywords
Artificial Intelligence-Enabled De Novo Design of Novel Compounds that Are Synthesizable.
Sign Up to like & getrecommendations! Published in 2022 at "Methods in molecular biology"
DOI: 10.1007/978-1-0716-1787-8_17
Abstract: Development of computer-aided de novo design methods to discover novel compounds in a speedy manner to treat human diseases has been of interest to drug discovery scientists for the past three decades. In the beginning, the… read more here.
Keywords: intelligence enabled; enabled novo; artificial intelligence; novo design ... See more keywords
Evolving methods for rational de novo design of functional RNA molecules.
Sign Up to like & getrecommendations! Published in 2019 at "Methods"
DOI: 10.1016/j.ymeth.2019.04.022
Abstract: Artificial RNA molecules with novel functionality have many applications in synthetic biology, pharmacy and white biotechnology. The de novo design of such devices using computational methods and prediction tools is a resource-efficient alternative to experimental… read more here.
Keywords: evolving methods; rna molecules; methods rational; novo design ... See more keywords
De Novo Design of Nurr1 Agonists via Fragment-Augmented Generative Deep Learning in Low-Data Regime.
Sign Up to like & getrecommendations! Published in 2023 at "Journal of medicinal chemistry"
DOI: 10.1021/acs.jmedchem.3c00485
Abstract: Generative neural networks trained on SMILES can design innovative bioactive molecules de novo. These so-called chemical language models (CLMs) have typically been trained on tens of template molecules for fine-tuning. However, it is challenging to… read more here.
Keywords: nurr1 agonists; low data; novo design; fragment augmented ... See more keywords
De Novo Design of a Pt Nanocatalyst on a Conjugated Microporous Polymer-Coated Honeycomb Carrier for Oxidation of Hydrogen Isotopes.
Sign Up to like & getrecommendations! Published in 2022 at "ACS applied materials & interfaces"
DOI: 10.1021/acsami.1c19844
Abstract: A booming demand for energy highlights the importance of an emergency cleanup system in the nuclear industry or hydrogen-energy sector to reduce the risk of hydrogen explosion and decrease tritium emission. The properties of the… read more here.
Keywords: oxidation; microporous polymer; novo design; hydrogen ... See more keywords
De novo design of a hyperstable non-natural protein-ligand complex with sub-Å accuracy.
Sign Up to like & getrecommendations! Published in 2017 at "Nature chemistry"
DOI: 10.1038/nchem.2846
Abstract: Protein catalysis requires the atomic-level orchestration of side chains, substrates and cofactors, and yet the ability to design a small-molecule-binding protein entirely from first principles with a precisely predetermined structure has not been demonstrated. Here… read more here.
Keywords: protein; design hyperstable; ligand; novo design ... See more keywords
De novo design of a reversible phosphorylation-dependent switch for membrane targeting
Sign Up to like & getrecommendations! Published in 2021 at "Nature Communications"
DOI: 10.1038/s41467-021-21622-5
Abstract: Modules that switch protein-protein interactions on and off are essential to develop synthetic biology; for example, to construct orthogonal signaling pathways, to control artificial protein structures dynamically, and for protein localization in cells or protocells.… read more here.
Keywords: switch; membrane targeting; reversible phosphorylation; novo design ... See more keywords