Related papers: p-Adic Structure of the Genetic Code
Protein design is a technique to engineer proteins by modifying their sequence to obtain novel functionalities. In this method, amino acids in the sequence are permutated to find the low energy states satisfying the configuration. However,…
Although several synonymous codons can encode the same aminoacid, this symmetry is generally broken in natural genetic systems. In this article, we show that the symmetry breaking can result from selective pressures due to the violation of…
An approach for approximately calculating the number of genes in a genome is presented, which takes into account the average protein length expected for the species. A number of virus, bacterial and eukaryotic genomes are scrutinized.…
The evolution in coding DNA sequences brings new flexibility and freedom to the codon words, even as the underlying nucleotides get significantly ordered. These curious contra-rules of gene organisation are observed from the distribution of…
The native state structures of globular proteins are stable and well-packed indicating that self-interactions are favored over protein-solvent interactions under folding conditions. We use this as a guiding principle to derive the geometry…
Proteins are intricate molecular machines whose complexity arises from the heterogeneity of the amino acid building blocks and their dynamic network of many-body interactions. These nanomachines gain function when put in the context of a…
Comprehensive knowledge of protein-ligand interactions should provide a useful basis for annotating protein functions, studying protein evolution, engineering enzymatic activity, and designing drugs. To investigate the diversity and…
Composed of amino acid chains that influence how they fold and thus dictating their function and features, proteins are a class of macromolecules that play a central role in major biological processes and are required for the structure,…
We review the recent progress in computational approaches to protein design which builds on advances in statistical-mechanical protein folding theory. In particular, we evaluate the degeneracy of the protein code (i.e. how many sequences…
A plausible architecture of an ancient genetic code is derived from an extended base triplet vector space over the Galois field of the extended base alphabet {D, G, A, U, C}, where the letter D represents one or more hypothetical bases with…
The Automated Protein Structure Analysis (APSA) method is used for the classification of supersecondary structures. Basis for the classification is the encoding of three-dimensional (3D) residue conformations into a 16-letter code (3D-1D…
Protein structure is central to biological function, and enabling multimodal protein models requires joint reasoning over sequence, structure, and function. A key barrier is the lack of principled protein structure tokenizers (PSTs):…
Given the amino acid sequence of a protein, researchers often infer its structure and function by finding homologous, or evolutionarily-related, proteins of known structure and function. Since structure is typically more conserved than…
Convolutional codes are constructed, designed and analysed using row and/or block structures of unit algebraic schemes. Infinite series of such codes and of codes with specific properties are derived. Properties are shown algebraically and…
In this study, the distributions of protein structure classes (or folding types) of experimentally determined structures from a legacy dataset and a comprehensive database (SCOP) are modeled precisely with geometric constructs such as…
Two genomes over the same set of gene families form a canonical pair when each of them has exactly one gene from each family. Different distances of canonical genomes can be derived from a structure called breakpoint graph, which represents…
Transcription factor proteins bind specific DNA sequences to control the expression of genes. They contain DNA binding domains which belong to several super-families, each with a specific mechanism of DNA binding. The total number of…
Proteins are composed of chains of amino acids that fold into complex three-dimensional structures. Several key features, such as the radius of gyration, fraction of core amino acids $f_{\rm core}$, packing fraction $\langle \phi\rangle$ of…
In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques,…
A hypothesis of the evolution of the genetic code is proposed, the leading mechanism of which is the nucleotide spontaneous damage leading to AT-enrichment of the genome. The hypothesis accounts for stability of the genetic code towards…