Related papers: Symmetry Scheme for Amino Acid Codons
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 origin of life is one of the greatest mysteries. The mechanism for the synthesis of DNA is synonymous with the chemical origin of life, and theories have been developed along many lines of reasoning, but resolving all requirements…
A Profile Mixture Model is a model of protein evolution, describing sequence data in which sites are assumed to follow many related substitution processes on a single evolutionary tree. The processes depend in part on different amino acid…
A two amino acid (hydrophobic and polar) scheme is used to perform the design on target conformations corresponding to the native states of twenty single chain proteins. Strikingly, the percentage of successful identification of the nature…
The global chaos caused by the 19 July 2024 technology meltdown highlights the need for a theory of what large-scale cohesive behaviors -- dangerous or desirable -- could suddenly emerge from future systems of interacting humans, machinery…
In this paper we inititate the study of abstract simplicial complexes which are initial segments of qualitative probability orders. This is a natural class that contains the threshold complexes and is contained in the shifted complexes, but…
We present A-CODE, a fully atomic unified one-stage protein co-design model that simultaneously refines discrete atom types and continuous atom coordinates. Unlike predominant two-stage methods that cascade structure design with amino…
The GC-content is very variable in different genome regions and species but although many hypothesis we still do not know the reason why. Here we show that a relationship exists with the mutation rate, in particular we noticed a new…
A method based on mapping a symbolic sequence into a set of patterns (strings resulting from the sequence parsing) is proposed as a tool for the reconstruction of ancestral sequences. The set union of patterns comprises all the patterns…
We use algorithmic methods from online learning to explore some important objects at the intersection of model theory and combinatorics, and find natural ways that algorithmic methods can detect and explain (and improve our understanding…
A general strategy is described for finding which amino acid sequences have native states in a desired conformation (inverse design). The approach is used to design sequences of 48 hydrophobic and polar aminoacids on three-dimensional…
The correlations of primary and secondary structures were analyzed using proteins with known structure from Protein Data Bank. The correlation values of amino acid type and the eight secondary structure types at distant position were…
The atomic structure and mechanical properties of the carbyne (monatomic linear chains), containing from 2 to 21 carbon atoms, are theoretically investigated by ab-initio methods. We demonstrate the existence of a stable cumulene-structure…
Algorithms that detect covariance between pairs of columns in multiple sequence alignments are commonly employed to predict functionally important residues and structural contacts. However, the assumption that co-variance only occurs…
The genetic code has a high level of error robustness. Using values of hydrophobicity scales as a proxy for amino acid character, and the Mean Square measure as a function quantifying error robustness, a value can be obtained for a genetic…
We give an asymptotic formula for the number of monic Eisenstein polynomials of odd prime degree satisfying an additional condition that arises in the study of the genus number of an algebraic number field.
We apply here the principle of affine symmetry to the nested fullerene cages (carbon onions) that arise in the context of carbon chemistry. Previous work on affine extensions of the icosahedral group has revealed a new organisational…
It is shown that the category of \emph{semi-biproducts} of monoids is equivalent to the category of \emph{pseudo-actions}. A semi-biproduct of monoids is a new notion, obtained through generalizing a biproduct of commutative monoids. By…
The number of protein structures is far less than the number of sequences. By imposing simple generic features of proteins (low energy and compaction) on all possible sequences we show that the structure space is sparse compared to the…
This study introduces SECODA, a novel general-purpose unsupervised non-parametric anomaly detection algorithm for datasets containing continuous and categorical attributes. The method is guaranteed to identify cases with unique or sparse…