ArticlePloS one2014
BioGPS descriptors for rational engineering of enzyme promiscuity and structure based bioinformatic analysis.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- A Computational Approach to Identify Novel Protein Targets Uncovers New Potential Mechanisms of Action of Mirtazapine S(+) and R(-) Enantiomers in Rett Syndrome.Journal of neurochemistry · 2025Article
- Enzymatic Synthesis and Structural Modeling of Bio-Based Oligoesters as an Approach for the Fast Screening of Marine Biodegradation and Ecotoxicity.International journal of molecular sciences · 2024Article
- Advances in ligand-specific biosensing for structurally similar molecules.Cell systems · 2023Review
- A platform for target prediction of phenotypic screening hit molecules.Journal of molecular graphics & modelling · 2020Article
- A Computational Method to Propose Mutations in Enzymes Based on Structural Signature Variation (SSV).International journal of molecular sciences · 2019Article
- Zymophore identification enables the discovery of novel phenylalanine ammonia lyase enzymes.Scientific reports · 2017Article
- Detecting similar binding pockets to enable systems polypharmacology.PLoS computational biology · 2017Article
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Authors and funding
7 authors.
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Abstract
A new bioinformatic methodology was developed founded on the Unsupervised Pattern Cognition Analysis of GRID-based BioGPS descriptors (Global Positioning System in Biological Space). The procedure relies entirely on three-dimensional structure analysis of enzymes and does not stem from sequence or structure alignment. The BioGPS descriptors account for chemical, geometrical and physical-chemical features of enzymes and are able to describe comprehensively the active site of enzymes in terms of "pre-organized environment" able to stabilize the transition state of a given reaction. The efficiency of this new bioinformatic strategy was demonstrated by the consistent clustering of four different Ser hydrolases classes, which are characterized by the same active site organization but able to catalyze different reactions. The method was validated by considering, as a case study, the engineering of amidase activity into the scaffold of a lipase. The BioGPS tool predicted correctly the properties of lipase variants, as demonstrated by the projection of mutants inside the BioGPS "roadmap".
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