Related papers: A unified statistical model of protein multiple se…
Global coevolutionary models of homologous protein families, as constructed by direct coupling analysis (DCA), have recently gained popularity in particular due to their capacity to accurately predict residue-residue contacts from sequence…
The possibility of deriving the contact potentials between amino acids from their frequencies of occurence in proteins is discussed in evolutionary terms. This approach allows the use of traditional thermodynamics to describe such…
The similarity in the three-dimensional structures of homologous proteins imposes strong constraints on their sequence variability. It has long been suggested that the resulting correlations among amino acid compositions at different…
Multisite protein phosphorylation plays a pivotal role in regulating cellular signaling and decision-making processes. In this study, we focus on the mathematical underpinnings and informational aspects of sequential, distributive…
To confer high specificity and affinity in binding, contacts at interfaces between two interacting macromolecules are expected to exhibit pair preferences for types of atoms or residues. Here we quantify these preferences by measuring the…
Multiple Sequence Alignment (MSA) plays a pivotal role in unveiling the evolutionary trajectories of protein families. The accuracy of protein structure predictions is often compromised for protein sequences that lack sufficient homologous…
The coding space of protein sequences is shaped by evolutionary constraints set by requirements of function and stability. We show that the coding space of a given protein family--the total number of sequences in that family--can be…
Rapid development of modern sequencing platforms enabled an unprecedented growth of protein families databases. The abundance of sets composed of hundreds of thousands sequences is a great challenge for multiple sequence alignment…
Is protein secondary structure primarily determined by local interactions between residues closely spaced along the amino acid backbone, or by non-local tertiary interactions? To answer this question we have measured the entropy densities…
The Method of Successive Approximations (MSA) is a fixed-point iterative method used to solve stochastic optimal control problems. It is an indirect method based on the conditions derived from the Stochastic Maximum Principle (SMP), an…
Background: Designing amino acid sequences that are stable in a given target structure amounts to maximizing a conditional probability. A straightforward approach to accomplish this is a nested Monte Carlo where the conformation space is…
The primary structure of proteins, that is their sequence, represents one of the most abundant set of experimental data concerning biomolecules. The study of correlations in families of co--evolving proteins by means of an inverse…
Proteins populate a manifold in the high-dimensional sequence space whose geometrical structure guides their natural evolution. Leveraging recently-developed structure prediction tools based on transformer models, we first examine the…
We propose a metric for the space of multiple sequence alignments that can be used to compare two alignments to each other. In the case where one of the alignments is a reference alignment, the resulting accuracy measure improves upon…
Time Series Alignment is a critical task in signal processing with numerous real-world applications. In practice, signals often exhibit temporal shifts and scaling, making classification on raw data prone to errors. This paper introduces a…
Advances in bio-technology have made available massive amounts of functional, structural and genomic data for many biological sequences. This increased availability of heterogeneous biological data has resulted in biological applications…
Recognition of pathogens relies on families of proteins showing great diversity. Here we construct maximum entropy models of the sequence repertoire, building on recent experiments that provide a nearly exhaustive sampling of the IgM…
Understanding the relationship between protein sequence, function, and stability is a fundamental problem in biology. While high-throughput methods have produced large numbers of sequence-function pairs, functional assays do not distinguish…
Sequence alignment is common nowadays as it is used in many fields to determine how closely two sequences are related and at times to see how little they differ. In computational biology / Bioinformatics, there are many algorithms developed…
Proteins are the basic building blocks of life. They usually perform functions by folding to a particular structure. Understanding the folding process could help the researchers to understand the functions of proteins and could also help to…