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Rossmann-toolbox: a deep learning-based protocol for the prediction and design of cofactor specificity in Rossmann fold proteins.

ABSTRACT: The Rossmann fold enzymes are involved in essential biochemical pathways such as nucleotide and amino acid metabolism. Their functioning relies on interaction with cofactors, small nucleoside-based compounds specifically recognized by a conserved βαβ motif shared by all Rossmann fold proteins. While Rossmann methyltransferases recognize only a single cofactor type, the S-adenosylmethionine, the oxidoreductases, depending on the family, bind nicotinamide (nicotinamide adenine dinucleotide, nicotinamide adenine dinucleotide phosphate) or flavin-based (flavin adenine dinucleotide) cofactors. In this study, we showed that despite its short length, the βαβ motif unambiguously defines the specificity towards the cofactor. Following this observation, we trained two complementary deep learning models for the prediction of the cofactor specificity based on the sequence and structural features of the βαβ motif. A benchmark on two independent test sets, one containing βαβ motifs bearing no resemblance to those of the training set, and the other comprising 38 experimentally confirmed cases of rational design of the cofactor specificity, revealed the nearly perfect performance of the two methods. The Rossmann-toolbox protocols can be accessed via the webserver at https://lbs.cent.uw.edu.pl/rossmann-toolbox and are available as a Python package at https://github.com/labstructbioinf/rossmann-toolbox.

SUBMITTER: Kaminski K

PROVIDER: S-EPMC8769691 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundDysphonia influences the quality of life by interfering with communication. However, a laryngoscopic examination is expensive and not readily accessible in primary care units. Experienced laryngologists are required to achieve an accurate diagnosis.ObjectiveThis study sought to detect various vocal fold diseases through pathological voice recognition using artificial intelligence.MethodsWe collected 189 normal voice samples and 552 samples of individuals with voice disorders, including vocal atrophy (n=224), unilateral vocal paralysis (n=50), organic vocal fold lesions (n=248), and adductor spasmodic dysphonia (n=30). The 741 samples were divided into 2 sets: 593 samples as the training set and 148 samples as the testing set. A convolutional neural network approach was applied to train the model, and findings were compared with those of human specialists.ResultsThe convolutional neural network model achieved a sensitivity of 0.66, a specificity of 0.91, and an overall accuracy of 66.9% for distinguishing normal voice, vocal atrophy, unilateral vocal paralysis, organic vocal fold lesions, and adductor spasmodic dysphonia. Compared with the accuracy of human specialists, the overall accuracy rates were 60.1% and 56.1% for the 2 laryngologists and 51.4% and 43.2% for the 2 general ear, nose, and throat doctors.ConclusionsVoice alone could be used for common vocal fold disease recognition through a deep learning approach after training with our Mandarin pathological voice database. This approach involving artificial intelligence could be clinically useful for screening general vocal fold disease using the voice. The approach includes a quick survey and a general health examination. It can be applied during telemedicine in areas with primary care units lacking laryngoscopic abilities. It could support physicians when prescreening cases by allowing for invasive examinations to be performed only for cases involving problems with automatic recognition or listening and for professional analyses of other clinical examination results that reveal doubts about the presence of pathologies.

Dataset Information

Rossmann-toolbox: a deep learning-based protocol for the prediction and design of cofactor specificity in Rossmann fold proteins.

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