Profile analysis is a method for detecting distantly related proteins by sequence comparison. The basis for comparison is not only the customary Dayhoff mutational-distance matrix but also the results of structural studies and information implicit in the alignments of the sequences of families of similar proteins. This information is expressed in a… (More)
We have developed a method for calculating the stability in water of protein structures, starting from their atomic coordinates. The contribution of each protein atom to the solvation free energy is estimated as the product of the accessibility of the atom to solvent and its atomic solvation parameter. Applications of the method include estimates of the… (More)
The amino acid sequence of the rod portion of nematode myosin, deduced for the sequence of the unc-54 heavy chain gene of Caenorhabditis elegans, is highly repetitive and has the characteristics of an alpha-helical coiled coil. The molecular surface contains alternate clusters of positive and negative charge. Interactions between charge clusters on adjacent… (More)
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.
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)
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)