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A review of mathematical representations of biomolecular data.

ABSTRACT: Recently, machine learning (ML) has established itself in various worldwide benchmarking competitions in computational biology, including Critical Assessment of Structure Prediction (CASP) and Drug Design Data Resource (D3R) Grand Challenges. However, the intricate structural complexity and high ML dimensionality of biomolecular datasets obstruct the efficient application of ML algorithms in the field. In addition to data and algorithm, an efficient ML machinery for biomolecular predictions must include structural representation as an indispensable component. Mathematical representations that simplify the biomolecular structural complexity and reduce ML dimensionality have emerged as a prime winner in D3R Grand Challenges. This review is devoted to the recent advances in developing low-dimensional and scalable mathematical representations of biomolecules in our laboratory. We discuss three classes of mathematical approaches, including algebraic topology, differential geometry, and graph theory. We elucidate how the physical and biological challenges have guided the evolution and development of these mathematical apparatuses for massive and diverse biomolecular data. We focus the performance analysis on protein-ligand binding predictions in this review although these methods have had tremendous success in many other applications, such as protein classification, virtual screening, and the predictions of solubility, solvation free energies, toxicity, partition coefficients, protein folding stability changes upon mutation, etc.

SUBMITTER: Nguyen DD

PROVIDER: S-EPMC7081943 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

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A review of mathematical representations of biomolecular data.

Nguyen Duc Duy DD Cang Zixuan Z Wei Guo-Wei GW

Physical chemistry chemical physics : PCCP 20200201 8

Recently, machine learning (ML) has established itself in various worldwide benchmarking competitions in computational biology, including Critical Assessment of Structure Prediction (CASP) and Drug Design Data Resource (D3R) Grand Challenges. However, the intricate structural complexity and high ML dimensionality of biomolecular datasets obstruct the efficient application of ML algorithms in the field. In addition to data and algorithm, an efficient ML machinery for biomolecular predictions must ...[more]

PMID: 32067019

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Project description:BACKGROUND:Sexual mixing between heterogeneous population subgroups is an integral component of mathematical models of sexually transmitted infections (STIs). This study compares the fit of different mixing representations to survey data and the impact of different mixing assumptions on the predicted benefits of hypothetical human papillomavirus (HPV) vaccine strategies. METHODS:We compared novel empirical (data-driven) age mixing structures with the more commonly-used assortative-proportionate (A-P) mixing structure. The A-P mixing structure assumes that a proportion of sexual contacts - known as the assortativity constant, typically estimated from survey data or calibrated - occur exclusively within one's own age group and the remainder mixes proportionately among all age groups. The empirical age mixing structure was estimated from the National Survey on Sexual Attitudes and Lifestyles 3 (Natsal-3) using regression methods, and the assortativity constant was estimated from Natsal-3 as well. Using a simplified HPV transmission model under each mixing assumption, we calibrated the model to British HPV16 prevalence data, then estimated the reduction in steady-state prevalence and the number of infections averted due to expanding HPV vaccination from 12- through 26-year-old females alone to 12-year-old males or 27- to 39-year-old females. RESULTS:Empirical mixing provided a better fit to the Natsal-3 data than the best-fitting A-P structure. Using the model with empirical mixing as a reference, the model using the A-P structure often under- or over-estimated the benefits of vaccination, in one case overestimating by 2-fold the number of infections prevented due to extended female catch-up in a high vaccine uptake setting. CONCLUSIONS:An empirical mixing structure more accurately represents sexual mixing survey data, and using the less accurate, yet commonly-used A-P structure has a notable effect on estimates of HPV vaccination benefits. This underscores the need for mixing structures that are less dependent on unverified assumptions and are directly informed by sexual behavior data.

Dataset Information

A review of mathematical representations of biomolecular data.

Publications

A review of mathematical representations of biomolecular data.

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