Predictive, structure-based model of amino acid recognition by nonribosomal peptide synthetase adenylation domains.

By G. Challis, Jacques Ravel, C. Townsend. Chemistry and Biology, 2000

731 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology, Pharmacology

View Paper: https://www.semanticscholar.org/paper/2f29fa77c19cf54cf36d531097233b17ea4d88e1

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

1. J. Loper
2. H. Gross
3. J. Bennett
4. N. Keller
5. G. Turner
6. Oliver Kohlbacher
7. Cheng-Yu Chen
8. Amy C. Anderson

In Molecular Biology

1. J. Loper
2. H. Gross
3. Tilmann Weber
4. Wolfgang Wohlleben
5. Oliver Kohlbacher
6. N. Keller
7. J. Bennett
8. G. Turner

In Pharmacology

1. J. Loper
2. H. Gross
3. N. Keller
4. J. Bennett
5. G. Turner
6. Tilmann Weber
7. Stefan Lutz

Citations in the corpus

• Genomic analysis of antifungal metabolite production by Pseudomonas fluorescens Pf-5 (2007, positive): “These signature motifs can be identified using webbased bioinformatic algorithms (Ansari et al. 2004; Challis et al. 2000 ) and, because of the colinearity rule, they can be used to predict the order, composition and number of amino acids in the final peptide product.”
• Cyanobacterial peptides - nature's own combinatorial biosynthesis. (2006, background): “…of the phenylalanine binding pocket of the activating domain of the first module of gramicidin S synthetase has led to an amino acid contact residue code permitting the prediction of substrates in NRPS adenylation domains (Stachelhaus et al., 1999; Challis et al., 2000; Lautru & Challis, 2004).”
• Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using transductive support vector machines (TSVMs) (2005, background): “(6) into account.”
• Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2) (2002, methodology): “For example, using predictive models for substrate amino-acid recognitio”
• Fungal secondary metabolism — from biochemistry to genomics (2005, methodology): “In bacteria, prediction of NRPS products has been partially successful through the use of a derivation of a module-recognition code that is based on correlation of NRPS adenylation domain structure to a particular amino aci”
• NRPS-PKS: a knowledge-based resource for analysis of NRPS/PKS megasynthases (2004, methodology): “edu/~nrps/) which predicts specificity of adenylation domains using a similar knowledge-based approach ( 21 ).”
• Computational structure-based redesign of enzyme activity (2009, methodology): “Alternative methods for the redesign of NRPS enzymes include domain swapping/directed evolution (7) and various sequence-based methods (24, 25).”