AIMC Topic: Substrate Specificity
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Machine Learning Identifies Chemical Characteristics That Promote Enzyme Catalysis.
Journal of the American Chemical Society
Feb 21, 2019
Despite tremendous progress in understanding and engineering enzymes, knowledge of how enzyme structures and their dynamics induce observed catalytic properties is incomplete, and capabilities to engineer enzymes fall far short of industrial needs. H...
Computational methods and tools to predict cytochrome P450 metabolism for drug discovery.
Chemical biology & drug design
Jan 15, 2019
In this review, we present important, recent developments in the computational prediction of cytochrome P450 (CYP) metabolism in the context of drug discovery. We discuss in silico models for the various aspects of CYP metabolism prediction, includin...
Data-driven supervised learning of a viral protease specificity landscape from deep sequencing and molecular simulations.
Proceedings of the National Academy of Sciences of the United States of America
Dec 26, 2018
Biophysical interactions between proteins and peptides are key determinants of molecular recognition specificity landscapes. However, an understanding of how molecular structure and residue-level energetics at protein-peptide interfaces shape these l...
Classification, substrate specificity and structural features of D-2-hydroxyacid dehydrogenases: 2HADH knowledgebase.
BMC evolutionary biology
Dec 22, 2018
BACKGROUND: The family of D-isomer specific 2-hydroxyacid dehydrogenases (2HADHs) contains a wide range of oxidoreductases with various metabolic roles as well as biotechnological applications. Despite a vast amount of biochemical and structural data...
Discovering de novo peptide substrates for enzymes using machine learning.
Nature communications
Dec 7, 2018
The discovery of peptide substrates for enzymes with exclusive, selective activities is a central goal in chemical biology. In this paper, we develop a hybrid computational and biochemical method to rapidly optimize peptides for specific, orthogonal ...
A machine learning approach for reliable prediction of amino acid interactions and its application in the directed evolution of enantioselective enzymes.
Scientific reports
Nov 13, 2018
Directed evolution is an important research activity in synthetic biology and biotechnology. Numerous reports describe the application of tedious mutation/screening cycles for the improvement of proteins. Recently, knowledge-based approaches have fac...
Predictable and precise template-free CRISPR editing of pathogenic variants.
Nature
Nov 7, 2018
Following Cas9 cleavage, DNA repair without a donor template is generally considered stochastic, heterogeneous and impractical beyond gene disruption. Here, we show that template-free Cas9 editing is predictable and capable of precise repair to a pre...
Application of molecular docking and PSO-SVR intelligent approaches in antimalarial activity prediction of enantiomeric cycloguanil analogues.
SAR and QSAR in environmental research
Nov 1, 2018
A series of antifolate compounds, i.e. 1-(4-chlorophenyl)-6,6-dimethyl-1,3,5-triazine-2,4-diamine, or cycloguanil analogues, have shown effective inhibiting properties against Plasmodium falciparum dihydrofolate reductase (PfDHFR). In this work, the ...
Algorithms
Proguanil
Reproducibility of Results
Tetrahydrofolate Dehydrogenase
Folic Acid Antagonists
Molecular Docking Simulation
Molecular Structure
Substrate Specificity
Antimalarials
Triazines
Protein Binding
Enzyme Inhibitors
Plasmodium falciparum
Quantitative Structure-Activity Relationship
Stereoisomerism
Machine Learning
A computational method for prediction of xylanase enzymes activity in strains of Bacillus subtilis based on pseudo amino acid composition features.
PloS one
Oct 22, 2018
Xylanases are hydrolytic enzymes which based on physicochemical properties, structure, mode of action and substrate specificities are classified into various glycoside hydrolase (GH) families. The purpose of this study is to show that the activity of...
The use of marine-derived fungi for preparation of enantiomerically pure alcohols.
Applied microbiology and biotechnology
Dec 20, 2017
A highly enantioselective and minimally polluting approach to optically pure chiral alcohols is developed using cheap, readily available and sustainable marine-derived fungi as catalysts. An evaluation of the synthetic potential of 13 Chinese marine ...
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