title: Convert your favorite protein modeling program into a mutation predictor: "MODICT".
abstract: BACKGROUND
  Predict whether a mutation is deleterious based on the custom 3D model of a protein.
  
  
  RESULTS
  We have developed MODICT, a mutation prediction tool which is based on per residue RMSD (root mean square deviation) values of superimposed 3D protein models. Our mathematical algorithm was tested for 42 described mutations in multiple genes including renin (REN), beta-tubulin (TUBB2B), biotinidase (BTD), sphingomyelin phosphodiesterase-1 (SMPD1), phenylalanine hydroxylase (PAH) and medium chain Acyl-Coa dehydrogenase (ACADM). Moreover, MODICT scores corresponded to experimentally verified residual enzyme activities in mutated biotinidase, phenylalanine hydroxylase and medium chain Acyl-CoA dehydrogenase. Several commercially available prediction algorithms were tested and results were compared. The MODICT PERL package and the manual can be downloaded from https://github.com/IbrahimTanyalcin/MODICT .
  
  
  CONCLUSIONS
  We show here that MODICT is capable tool for mutation effect prediction at the protein level, using superimposed 3D protein models instead of sequence based algorithms used by POLYPHEN and SIFT.
authors.affiliation: Center for Medical Genetics, UZ Brussel, Laarbeeklaan 101, Brussel, 1090, Belgium. itanyalc@vub.ac.be.|Neurogenetics Research Group, Reproduction Genetics and Regenerative Medicine Research Group, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, Brussel, 1090, Belgium. itanyalc@vub.ac.be.
authors.forename: Ibrahim
authors.initials: I
authors.lastname: Tanyalcin
authors.affiliation: Center for Medical Genetics, Reproduction and Genetics, Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel (VUB), UZ Brussel, Laarbeeklaan 101, Brussel, 1090, Belgium.
authors.forename: Katrien
authors.initials: K
authors.lastname: Stouffs
authors.affiliation: Center for Medical Genetics, Reproduction and Genetics, Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel (VUB), UZ Brussel, Laarbeeklaan 101, Brussel, 1090, Belgium.
authors.forename: Dorien
authors.initials: D
authors.lastname: Daneels
authors.affiliation: Center for Human Genetics, KU Leuven and University Hospitals Leuven, Herestraat 49, Leuven, 3000, Belgium.
authors.forename: Carla
authors.initials: C
authors.lastname: Al Assaf
authors.affiliation: Center for Medical Genetics, Reproduction and Genetics, Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel (VUB), UZ Brussel, Laarbeeklaan 101, Brussel, 1090, Belgium.
authors.forename: Willy
authors.initials: W
authors.lastname: Lissens
authors.affiliation: Center for Medical Genetics, UZ Brussel, Laarbeeklaan 101, Brussel, 1090, Belgium.|Neurogenetics Research Group, Reproduction Genetics and Regenerative Medicine Research Group, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, Brussel, 1090, Belgium.|Pediatric Neurology Unit, Department of Pediatrics, UZ Brussel, Laarbeeklaan 101, Brussel, 1090, Belgium.
authors.forename: Anna
authors.initials: A
authors.lastname: Jansen
authors.affiliation: Center for Medical Genetics, Reproduction and Genetics, Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel (VUB), UZ Brussel, Laarbeeklaan 101, Brussel, 1090, Belgium.
authors.forename: Alexander
authors.initials: A
authors.lastname: Gheldof
mesh_terms: D042964:Acyl-CoA Dehydrogenase / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D008958:Models, Molecular; D009154:Mutation / Q000235:genetics*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000235:genetics*; D012083:Renin / Q000235:genetics; D012984:Software; D014404:Tubulin / Q000235:genetics
chemical_list: D011506:Proteins; D014404:Tubulin; D042964:Acyl-CoA Dehydrogenase; D012083:Renin
keywords: 3D protein model; Bioinformatics; Prediction