Related papers: Capturing coevolutionary signals in repeat protein…
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…
We study a large data set of protein structure ensembles of very diverse sizes determined by nuclear magnetic resonance. By examining the distance-dependent correlations in the displacement of residues pairs and conducting finite size…
Inferences about the evolution of continuous traits based on reconstruction of ancestral states has often been considered more error-prone than analysis of independent contrasts. Here we show that both methods in fact yield identical…
Genome rearrangement is a common model for molecular evolution. In this paper, we consider the Pairwise Rearrangement problem, which takes as input two genomes and asks for the number of minimum-length sequences of permissible operations…
Interacting particle systems undergoing repeated mutation and selection steps model genetic evolution, and also describe a broad class of sequential Monte Carlo methods. The genealogical tree embedded into the system is important in both…
Motivation: Thanks to the recent advances in structural biology, nowadays three-dimensional structures of various proteins are solved on a routine basis. A large portion of these contain structural repetitions or internal symmetries. To…
The dynamical systems found in Nature are rarely isolated. Instead they interact and influence each other. The coupling functions that connect them contain detailed information about the functional mechanisms underlying the interactions and…
Learning language of protein sequences, which captures non-local interactions between amino acids close in the spatial structure, is a long-standing bioinformatics challenge, which requires at least context-free grammars. However, complex…
We propose a model that explains the hierarchical organization of proteins in fold families. The model, which is based on the evolutionary selection of proteins by their native state stability, reproduces patterns of amino acids conserved…
Successive whole genome duplications have recently been firmly established in all major eukaryote kingdoms. It is not clear, however, how such dramatic evolutionary process has contributed to shape the large scale topology of…
The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…
Predicting protein structure from the amino acid sequence has been a challenge with theoretical and practical significance in biophysics. Despite the recent progresses elicited by improved residue-residue contact prediction, contact-based…
Proteins are macromolecules that perform essential functions in all living organisms. Designing novel proteins with specific structures and desired functions has been a long-standing challenge in the field of bioengineering. Existing…
Motivation: The study of diverse enzyme superfamilies can provide important insight into the relationships between protein sequence, structure and function. It is often challenging, however, to discover these relationships across a large…
Many real-world systems give rise to a time series of symbols. The elements in a sequence can be generated by agents walking over a networked space so that whenever a node is visited the corresponding symbol is generated. In many situations…
Protein structure prediction remains a challenge in the field of computational biology. Traditional protein structure prediction approaches include template-based modelling (say, homology modelling, and threading), and ab initio. A…
Several technological applications require the translation of a protein into a nucleic acid that codes for it (``backtranslation''). The degeneracy of the genetic code makes this translation ambiguous; moreover, not every translation is…
In this paper we present a generative model for protein contact networks. The soundness of the proposed model is investigated by focusing primarily on mesoscopic properties elaborated from the spectra of the graph Laplacian. To complement…
Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer…
Protein one-dimensional (1D) structures such as secondary structure and contact number provide intuitive pictures to understand how the native three-dimensional (3D) structure of a protein is encoded in the amino acid sequence. However, it…