Convert your favorite protein modeling program into a mutation predictor: 'MODICT'
| Autor: | Carla Al Assaf, Ibrahim Tanyalcin, Willy Lissens, Alexander Gheldof, Dorien Daneels, Anna Jansen, Katrien Stouffs |
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| Přispěvatelé: | Public Health Sciences, Neurogenetics, Reproduction and Genetics, Clinical sciences, Faculty of Medicine and Pharmacy, Mental Health and Wellbeing research group, Basic (bio-) Medical Sciences |
| Jazyk: | angličtina |
| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Models Molecular Phenylalanine hydroxylase Computer science Bioinformatics Protein Conformation Dehydrogenase Computational biology medicine.disease_cause Biochemistry Acyl-CoA Dehydrogenase 03 medical and health sciences 0302 clinical medicine Protein structure Structural Biology Tubulin Renin medicine Humans Molecular Biology Root-mean-square deviation Gene ACADM chemistry.chemical_classification Genetics Mutation biology Applied Mathematics Acyl CoA dehydrogenase A protein Computational Biology Proteins Protein structure prediction Computer Science Applications 030104 developmental biology Enzyme chemistry Mutation (genetic algorithm) Protein model biology.protein Biotinidase 3D protein model Prediction 030217 neurology & neurosurgery Software |
| Zdroj: | BMC Bioinformatics |
| ISSN: | 1471-2105 |
| Popis: | Motivation:Predict whether a mutation is deleterious based on the custom 3D model of a protein.Methods:We have developed MGDIGT, a mutation prediction tool which isbased on per residue rmsd (root mean square deviation) values of superimposed3D protein models. Our mathematical algorithm was tested for 42 describedmutations in multiple genes including renin, beta-tubulin, biotinidase,sphingomyelin phosphodiesterase-1, phenylalanine hydroxylase and medium chainAcyl-Coa dehydrogenase. Moreover, modict scores corresponded toexperimentally verified residual enzyme activities in mutated biotinidase,phenylalanine hydroxylase and medium chain Acyl-CoA dehydrogenase. Severalcommercially available prediction algorithms were tested and results werecompared. The modict PERL package and the manual can be downloaded from https://github.com/MODICT/MODICT.Conclusion:We show here that modict is capable tool for mutation effectprediction at the protein level, using superimposed 3D protein models instead ofsequence based algorithms used by PGLYPHEN and SIFT. |
| Databáze: | OpenAIRE |
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