Stylus: A System for Evolutionary Experimentation Based on a Protein/Proteome Model with Non-Arbitrary Functional Constraints
Steps are illustrated for a vector protein (U+8C58) on the left, with analogous aspects of a real protein (PDB 1CQD) on the right. A) Codons in an open reading frame specify monomers (vectors or amino acids) that may form regular local structure (green) or irregular local structure (grey). In the vector world a simple rule determines which is the case: A vector becomes part of regular structure if and only if it forms a coherent vector triplet (indicated by green tiles below the sequence; see text). B) Vectors are joined to form paths with head and tail termini, just as amino acids are joined to form chains with amino and carboxyl termini (right panel derived from public domain images by Yassine Mrabet). C) Vector proteins consist of strokes (formed by runs of coherent vectors) joined by moves (formed by runs of incoherent vectors), in much the same way that real proteins consist of units of secondary structure joined by turns or loops. D) Final working forms, highlighting the segments shown above.