Related papers: Genetic Code: A New Understanding of Codon - Amino…
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…
Complex systems with tightly coadapted parts frequently appear in living systems and are difficult to account for through Darwinian evolution, that is random variation and natural selection, if the constituent parts are independently coded…
We present a scenario for the origin of biological coding. In this context, coding is a semiotic relationship between chemical information stored in one location that links to chemical information stored in a separate location. Coding…
We Propose 22 unique Solutions to the Genetic Code. An Alternative Cracking, from the Perspective of a Mathematician.
Each human genome is a 3 billion base pair set of encoding instructions. Decoding the genome using deep learning fundamentally differs from most tasks, as we do not know the full structure of the data and therefore cannot design…
Codes have been used for centuries to convey secret information.To a cryptanalyst, the interception of a code is only the first step in recovering a secret message.Deoxyribonucleic acid (DNA) is a biological and molecular code.Through the…
Using the shape space of codons and tRNAs we give a physical description of the genetic code evolution on the basis of the codon capture and ambiguous intermediate scenarios in a consistent manner. In the lowest dimensional version of our…
We present a structural data set of the 20 proteinogenic amino acids and their amino-methylated and acetylated (capped) dipeptides. Different protonation states of the backbone (uncharged and zwitterionic) were considered for the amino…
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…
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…
A molecular dynamics calculation of the amino acid polar requirement is presented and used to score the canonical genetic code. Monte Carlo simulation shows that this computational polar requirement has been optimized by the canonical…
A simple lattice model for proteins that allows for distinct sizes of the amino acids is presented. The model is found to lead to a significant number of conformations that are the unique ground state of one or more sequences or encodable.…
Rich information on the prebiotic evolution is still stored in contemporary genomic data. The statistical mechanism at the sequence level may play a significant role in the prebiotic evolution. Based on statistical analysis of genome…
A model for the information transfer from DNA to protein using quantum information and computation techniques is presented. DNA is modeled as the sender and proteins are modeled as the receiver of this information. On the DNA side, a…
Background/ Objectives: Resolving the origin of the genetic code is fundamental to understanding how life began its journey out of the chemical world. Since its deciphering some 60 years ago, there is still no general theory of the…
In order to extend the results obtained with minimal lattice models to more realistic systems, we study a model where proteins are described as a chain of 20 kinds of structureless amino acids moving in a continuum space and interacting…
Coding information is the main source of heterogeneity (non-randomness) in the sequences of bacterial genomes. This information can be naturally modeled by analysing cluster structures in the "in-phase" triplet distributions of relatively…
A theoretical construction of the genetic material establishes the unique and ideal character of DNA. A similar conclusion is reached for amino acids and proteins.
We perform geometrization of genetics by representing genetic information by points of the 4-adic {\it information space.} By well known theorem of number theory this space can also be represented as the 2-adic space. The process of…
The twenty protein coding amino acids are found in proteomes with different relative abundances. The most abundant amino acid, leucine, is nearly an order of magnitude more prevalent than the least abundant amino acid, cysteine. Amino acid…