Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/295857

Accurate informatic modeling of tooth enamel pellicle interactions by training substitution matrices with Mat4Pep

Horst, J. A.·Seto, J.·Oren, E. E.·Horst, O. V.·Hung, L.-H. H.·Samudrala, R.
View original source ↗Export metadata ↓

Abstract

MotivationProtein-hydroxyapatite interactions govern the development and homeostasis of teeth and bone. Characterization would enable design of peptides to regenerate mineralized tissues and control attachments such as ligaments and dental plaque. Progress has been limited because no available methods produce robust data for assessing phase interfaces.\n\nResultsWe show that tooth enamel pellicle peptides contain subtle sequence similarities that encode hydroxyapatite binding mechanisms, by segregating pellicle peptides from control sequences using our previously developed substitution matrix-based peptide comparison protocol (Oren et al., 2007), with improvements. Sampling diverse matrices, adding biological control sequences, and optimizing matrix refinement algorithms improves discrimination from 0.81 to 0.99 AUC in leave-one-out experiments. Other contemporary methods fail on this problem. We find hydroxyapatite interaction sequence patterns by applying the resulting selected refined matrix (\"pellitrix\") to cluster the peptides and build subgroup alignments. We identify putative hydroxyapatite maturation domains by application to enamel biomineralization proteins and prioritize putative novel pellicle peptides identified by In stageTip (iST) mass spectrometry. The sequence comparison protocol outperforms other contemporary options for this small and heterogeneous group, and is generalized for application to any group of peptides.\n\nAvailabilitySoftware to apply this protocol is freely available at github.com/JeremyHorst/Mat4Pep and compbio.org/protinfo/ Mat4Pep.\n\nContactjahorst@gmail.com, ram@compbio.org.\n\nSupplementary informationAvailable at Bioinformatics online.

Explore related subjects

bioinformaticsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Horst, J. A., Seto, J., Oren, E. E., Horst, O. V., Hung, L.-H. H., Samudrala, R.. 2018-04-06. Accurate informatic modeling of tooth enamel pellicle interactions by training substitution matrices with Mat4Pep. https://doi.org/10.1101/295857

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

The Almond Expression Atlas: A comprehensive multi-tissue transcriptomic resource for almond gene expression

Background: Improving crop adaptation and enhancing agronomic and quality traits requires a deeper understanding of gene expression regulation, for which expression atlases are valuable tools. Almond (Prunus dulcis (Mill.) D.A. Webb) is one of the most economically important tree nut crops worldwide. However, an integrated transcriptomic resource for this species is still lacking. Available data remain fragmented across independent studies, limiting their comparability and reuse. Results: Here, we present the first almond gene expression atlas: a comprehensive multi-tissue transcriptomic resource integrating publicly available RNA sequencing data. A total of 142 high-quality untreated and control samples from 17 independent projects were curated through a metadata standardization process and analyzed using a unified bioinformatics pipeline. Standardized expression profiles were generated for 25,225 annotated genes in the Prunus dulcis Texas v2.0 reference genome. The atlas integrates two complementary expression approaches: a median TPM approach capturing quantitative expression levels and a rank-based strategy implemented using the Bgee expression calling method, designed to improve comparability across heterogeneous datasets. This design enables the identification of tissue-specific candidate genes and the exploration of expression patterns across tissues and developmental stages. Its applicability is demonstrated through two use cases, highlighting its ability to identify biologically meaningful gene sets associated with bud dormancy transitions and to prioritize candidate reference genes for RT-qPCR normalization in almond. Conclusions: The Almond Expression Atlas v1.0 is publicly available through FruitDBase (fruitdbase.csic.es), providing an interactive platform for gene expression exploration and visualization. This resource supports functional genomics studies and facilitates candidate gene discovery in almond, while ensuring data traceability and promoting data reusability.

bioinformatics↗
bioRxiv2026

Leakage-Controlled Benchmarking of Variant Effect Predictors and Development of Gradient-Boosting Consensus Model

Single amino acid mutations are among the most common forms of genetic variation, with effects ranging from negligible to severe disruption of protein function. Accurate quantitative evaluation of protein variants therefore represents a key challenge in medicine and protein engineering. Computational variant effect predictors (VEPs) are widely used to prioritize missense variants, yet their fair comparison is hindered by data circularity, benchmarks restricted to human clinical annotations, and limited availability of code and training data, all of which can inflate apparent performance. Here, we reviewed 18 recent and 3 older, widely adopted variant effect predictors for reproducible benchmarking and assembled a rigorously curated, leakage-controlled Benchmark dataset by integrating clinically annotated human variants from ClinVar and Humsavar as well as cross-species variants with functional annotations. The evaluation on this dataset revealed a narrow overall performance range for the benchmarked tools (AUC 0.631-0.758) and a consistent drop from clinical to functional data. Surprisingly, several tools published two decades ago demonstrated comparable performance to mid-ranked modern predictors. Building on these results, we developed a gradient-boosting consensus model, PredictSNPprot, which achieved an AUC of 0.82 on a held-out test set, outperforming the original PredictSNP meta-predictor and the best individual state-of-the-art tool by 13.6 and 5.7 percentage points, respectively. The Benchmark dataset, including the predictions from the evaluated tools, is available at https://doi.org/10.5281/zenodo.23597130 and PredictSNPprot consensus predictor is available at https://github.com/loschmidt/PredictSNPprot.

bioinformatics↗
bioRxiv2026

MaCADEMIA: a software toolbox for single-molecule fluorescence image quantification

Single-molecule localisation microscopy (SMLM) is a powerful tool in molecular and cellular biology and part of the broad umbrella of super-resolution microscopy. A distinct feature of SMLM, is its capacity for deep quantification, beyond just spatial information, to copy number, stoichiometry, molecular interaction and dynamics in living cells. The hardware required is increasingly straightforward to implement. However, complexity remains in the image analysis where much remains fragmented across specialised software tools. Here, we present MaCADEMIA (Matlab Computational Analysis of Diffusion, Emitter Molecular Intensity and Abundance), a simple yet powerful toolbox of MATLAB functions and associated documentation to enable straightforward extraction of quantitative single-molecule information. MaCADEMIA performs ensemble particle detection achieving localisation accuracies down to 0.5 pixels Root mean squared error (RMSE) across wide signal-to-noise (SNR) ranges on standardised particle tracking benchmarks, consistently matching or exceeding the performance of 14 leading methods. Our integrated workflow enables molecular counting and stoichiometry determination through stepwise photobleaching analysis, mobility measurement via mean squared displacement, colocalisaton analysis and absolute protein copy number quantification using three-dimensional cellular models.

bioinformatics↗