Biology subjects

Vucetic, S.

Publications and source records attributed to Vucetic, S..

3 recordsLinked to original sources

bioRxiv2025

Evolutionary sparse learning with paired species contrast reveals the shared genetic basis of convergent traits

Cases abound in which nearly identical traits have appeared in distant species facing similar environments. These unmistakable examples of adaptive evolution offer opportunities to gain insight into their genetic origins and mechanisms through comparative analyses. Here, we present a novel comparative genomics approach to build genetic models that underlie the independent origins of convergent traits using evolutionary sparse learning. We test the hypothesis that common genes and sites are involved in the convergent evolution of two key traits: C4 photosynthesis in grasses and echolocation in mammals. Genetic models were highly predictive of independent cases of convergent evolution of C4 photosynthesis. These results support the involvement of sequence substitutions in many common genetic loci in the evolution of convergent traits studied. Genes contributing to genetic models for echolocation were highly enriched for functional categories related to hearing, sound perception, and deafness (P < 10-6); a pattern that has eluded previous efforts applying standard molecular evolutionary approaches. We conclude that phylogeny-informed machine learning naturally excludes apparent molecular convergences due to shared species history, enhances the signal-to-noise ratio for detecting molecular convergence, and empowers the discovery of common genetic bases of trait convergences.

evolutionary biology↗

bioRxiv2020

Multifaceted Analysis of Training and Testing Convolutional Neural Networks for Protein Secondary Structure Prediction

Protein secondary structure prediction remains a vital topic with improving accuracy and broad applications. By using deep learning algorithms, prediction methods not relying on structure templates were recently reported to reach as high as 87% accuracy on 3 labels (helix, sheet or coil). Due to lack of a widely accepted standard in secondary structure predictor development and evaluation, a fair comparison of predictors is challenging. A detailed examination of factors that contribute to higher accuracy is also lacking. In this paper, we present: (1) a new test set, Test2018, consisting of proteins from structures released in 2018 with less than 25% similar to any protein published before 2018; (2) a 4-layer convolutional neural network, SecNet, with an input window of {+/-}14 amino acids which was trained on proteins less than 25% identical to proteins in Test2018 and the commonly used CB513 test set; (3) a detailed ablation study where we reverse one algorithmic choice at a time in SecNet and evaluate the effect on the prediction accuracy; (4) new 4- and 5-label prediction alphabets that may be more practical for tertiary structure prediction methods. The 3-label accuracy of the leading predictors on both Test2018 and CB513 is 81-82%, while SecNets accuracy is 84% for both sets. The ablation study of different factors (evolutionary information, neural network architecture, and training hyper-parameters) suggests the best accuracy results are achieved with good choices for each of them while the neural network architecture is not as critical as long as it is not too simple. Protocols for generating and using unbiased test, validation, and training sets are provided. Our data sets, including input features and assigned labels, and SecNet software including third-party dependencies and databases, are downloadable from dunbrack.fccc.edu/ss and github.com/sh-maxim/ss.

bioinformatics↗

bioRxiv2018

A New Clustering and Nomenclature for Beta Turns Derived form High-Resolution Protein Structures

Protein loops connect regular secondary structures and contain 4-residue beta turns which represent 63% of the residues in loops. The commonly used classification of beta turns (Type I, I, II, II, VIa1, VIa2, VIb, and VIII) was developed in the 1970s and 1980s from analysis of a small number of proteins of average resolution, and represents only two thirds of beta turns observed in proteins (with a generic class Type IV representing the rest). We present a new clustering of beta turn conformations from a set of 13,030 turns from 1078 ultra-high resolution protein structures ([≤]1.2 [A]). Our clustering is derived from applying the DBSCAN and k-medoids algorithms to this data set with a metric commonly used in directional statistics applied to the set of dihedral angles from the second and third residues of each turn. We define 18 turn types compared to the 8 classical turn types in common use. We propose a new 2-letter nomenclature for all 18 beta-turn types using Ramachandran region names for the two central residues (e.g., A and D for alpha regions on the left side of the Ramachandran map and a and d for equivalent regions on the right-hand side; classical Type I turns are AD turns and Type I turns are ad). We identify 11 new types of beta turn, 5 of which are sub-types of classical beta turn types. Up-to-date statistics, probability densities of conformations, and sequence profiles of beta turns in loops were collected and analyzed. A library of turn types, BetaTurnLib18, and cross-platform software, BetaTurnTool18, which identifies turns in an input protein structure, are freely available and redistributable from dunbrack.fccc.edu/betaturn and github.com/sh-maxim/BetaTurn18. Given the ubiquitous nature of beta turns, this comprehensive study updates understanding of beta turns and should also provide useful tools for protein structure determination, refinement, and prediction programs.

bioinformatics↗