Related papers: The shrinking human protein coding complement: are…
Mass spectrometry provides a high-throughput approach to identify proteins in biological samples. A key step in the analysis of mass spectrometry data is to identify the peptide sequence that, most probably, gave rise to each observed…
The unbounded permutations of biological molecules, including proteins and their constituent peptides, presents a dilemma in identifying the components of complex biosamples. Sequence search algorithms used to identify peptide spectra can…
In the post-Moore era, the need for efficient solutions to non-deterministic polynomial-time (NP) problems is becoming more pressing. In this context, the Ising model implemented by the probabilistic computing systems with probabilistic…
Motivation: In mass spectrometry-based shotgun proteomics, protein quantification and protein identification are two major computational problems. To quantify the protein abundance, a list of proteins must be firstly inferred from the…
Protein-Protein Interactions (PPIs) perform essential roles in biological functions. Although some experimental techniques have been developed to detect PPIs, they suffer from high false positive and high false negative rates. Consequently,…
We describe and test an implicit solvent all-atom potential for simulations of protein folding and aggregation. The potential is developed through studies of structural and thermodynamic properties of 17 peptides with diverse secondary…
Proteins typically exist in complexes, interacting with other proteins or biomolecules to perform their specific biological roles. Research on single-chain protein modeling has been extensively and deeply explored, with advancements seen in…
Background The theoretical requirements for a genetic code were well defined and modeled by George Gamow and Francis Crick in the 50-es. Their models failed. However the valid Genetic Code, provided by Nirenberg and Matthaei in 1961,…
We investigated the error-minimization properties of putative primordial codes that consisted of 16 supercodons, with the third base being completely redundant, using a previously derived cost function and the error minimization percentage…
The problem of deciphering how low-level patterns (action potentials in the brain, amino acids in a protein, etc.) drive high-level biological features (sensorimotor behavior, enzymatic function) represents the central challenge of…
Degeneracy of the genetic code is a biological way to minimize effects of the undesirable mutation changes. Degeneration has a natural description on the 5-adic space of 64 codons $\mathcal{C}_5 (64) = \{n_0 + n_1 5 + n_2 5^2 : n_i = 1, 2,…
Proteins perform much of the work in living organisms, and consequently the development of efficient computational methods for protein representation is essential for advancing large-scale biological research. Most current approaches…
A number of recently discovered protein structures incorporate a rather unexpected structural feature: a knot in the polypeptide backbone. These knots are extremely rare, but their occurrence is likely connected to protein function in as…
Human physiology and pathology arise from the coordinated interactions of diverse single cells. However, analyzing single cells has been limited by the low sensitivity and throughput of analytical methods. DNA sequencing has recently made…
Accurately annotating and controlling protein function from sequence data remains a major challenge, particularly within homologous families where annotated sequences are scarce and structural variation is minimal. We present a two-stage…
Natural protein sequences that self-assemble to form globular structures are compact with high packing densities in the folded states. It is known that proteins unfold upon addition of denaturants, adopting random coil structures. The…
The genetic code refers to a rule that maps 64 codons to 20 amino acids. Nearly all organisms, with few exceptions, share the same genetic code, the standard genetic code (SGC). While it remains unclear why this universal code has arisen…
The human genome is incredibly information-rich, consisting of approximately 25,000 protein-coding genes spread out over 3.2 billion nucleotide base pairs contained within 24 unique chromosomes. The genome is important in maintaining…
The genetic code structure into distinct multiplet-classes as well as the numeric degeneracies of the latter are revealed by a two-step process. First, an empirical inventory of the degeneracies (of the shuffled multiplets) in two specific…
Protein folding is one of the age-old biological problems that refers to the mechanism of understanding and predicting how a protein's linear sequence of amino acids folds into its specific three dimensional structure.This structure is…