This paper describes a computer method that uses codon preference to help find protein coding regions in long DNA sequences. The method can distinguish between introns and exons and can help to detect sequencing errors.
The observation that the acid proteases contain two structurally equivalent lobes related by a dyad through the active centre has been extended to show that in endothiapepsin each lobe contains two similar halves related by a further local dyad. In lobe 1 22 pairs of alpha-carbons are equivalent with a root mean square deviation of 1.92 A. In lobe 2 17… (More)
Some globular proteins contain repeated structural patterns within the same polypeptide chain. Several enzymes have a pseudo-symmetric two-lobed architecture: a pair of connected but well separated domains with very similar structures are grouped round an approximate 2-fold symmetry axis close to the active centre. On a smaller scale the same motif may… (More)
We describe a new method of comparing sequences, based on the Needleman-Wunsch sequence alignment algorithm, which can detect similarities that are interrupted by insertions or deletions in either sequence. The sequences are compared by calculating for each pair of residues a score which represents the best local alignment bringing those residues into… (More)
The entropy-dynamics method seeks maxima for the entropy of the electron density for N atoms in a crystal cell, when the Fourier amplitudes are fixed, but their phases are unknown. By analogy with molecular dynamics, the effective potential energy is the negative entropy V = -NS. The kinetic energy is proportional to the squared velocities of the electron… (More)