The macroclass ABOX has a minimum of five, and an average of a little more than six, amphipathic alpha helices. One DSM of this type has been constructed to cover the domain length range of from 160 to 351 amino acids.

The macroclass APB has exactly four amphipathic helices of very nearly the same lengths. Twenty five DSMs (differing in sequence lengths) have been constructed to cover the domain length range of from 52 to 184 amino acids.

Additional DSMs have been added to the APB macroclass to model variations of the interleukin fold. In these DSMs, the first and the second helices are connected by a long loop. The third and the forth helices are also connected by a long loop. The second and the third helices are connected by a turn. Fifty-four DSMs have been constructed to cover the domain length range of from 62 to 359.

The macroclass DA has larger standard deviations (as compared to other alpha macroclasses) for the lengths of both the helices and the connecting loops and/or connecting loops plus turns. In DA, each alpha helix can be either buried or exposed. This macroclass is intended to include the more variable alpha domains for which the ABOX and APB are too constrained. Two DSMs have been constructed to cover the domain length range of from 124 to 600 amino acids.

The macroclass B6 has a minimum of five beta strands with sufficient length variation to cover that expected for a beta domain with a single beta sheet. Eight DSMs have been constructed to cover the domain length range from 73 to 278 amino acids.

The macroclass B9 has a minimum of eight beta strands with sufficient length variation to cover that expected for a beta domain with one or two beta sheets. Eight DSMs have been constructed to cover the domain length range from 103 to 370 amino acids.

The macroclass B12 has a minimum of eleven and a mean of twelve beta-strands with sufficient length variation to cover that expected for a beta domain with two beta sheets or a beta barrel. Eight DSMs have been constructed to cover the domain length range from 121 to 451 amino acids.

The macroclass BS has from five to twelve amphipathic strands exposed to the solvent. They form one beta sandwich and have lengths that are more constrained than in the B6, B9, and B12 macroclasses. Four DSMs have been constructed to cover the domain length range from 71 to 290 amino acids.

The macroclass BPROB4 has 4 small beta sheets arranged symmetrically in a cylinder. Each beta sheet has 4, and occasionally 3, beta strands. Eight DSMs have been constructed to cover the domain length of from 207 to 333 amino acids.

The macroclass BPROB5 has 5 small beta sheets arranged symmetrically in a cylinder. Each beta sheet has 4, and occasionally 3, beta strands. Eight DSMs have been constructed to cover the domain length of from 261 to 405 amino acids.

The macroclass BPROB6 has 6 small beta sheets arranged symmetrically in a cylinder. Each beta sheet has 4, and occasionally 3, beta strands. Eight DSMs have been constructed to cover the domain length of from 338 to 504 amino acids.

The macroclass BPROB7 has 7 small beta sheets arranged symmetrically in a cylinder. Each beta sheet has 4, and occasionally 3, beta strands. Eight DSMs have been constructed to cover the domain length of from 393 to 578 amino acids.

The macroclass BPROB8 has 8 small beta sheets arranged symmetrically in a cylinder. Each beta sheet has 4, and occasionally 3, beta strands. Eight DSMs have been constructed to cover the domain length of from 404 to 600 amino acids.

The macroclass BPROB9 has 9 small beta sheets arranged symmetrically in a cylinder. Each beta sheet has 4, and occasionally 3, beta strands. Eight DSMs have been constructed to cover the domain length of from 453 to 600 amino acids.

The macroclass PORIN has 16 to 18 beta strands. These strands form a transmembrane barrel. The amino acid propensities of these strands are significantly different from other globular beta proteins. Six DSMs are constructed to cover the domain length of from 283 to 462 amino acids.

The macroclass DB has large standard deviations on both the lengths and numbers of strands, connecting loops, and/or connecting loops plus turns as compared to other beta domain macroclasseses. This macroclass is intended to cover the more variable beta domains. Two DSMs have been constructed to cover the domain length range from 86 to 554 amino acids.

The macroclass SAB has alternating alpha helices and beta strands forming one layer consisting of an antiparallel beta sheet and another layer consisting of alpha helices. There are 2,3,4,5 strands in the beta sheet. Four DSMs have been constructed to cover the domain length range from 59 to 240 amino acids.

The macroclass AB5 has a sequence of beta strands alternating with alpha helices or long loops with a large standard deviation on the lengths of the beta strands. There are 4, 5, or 6 such repeats. Fifteen DSMs have been constructed to cover the domain length range from 107 to 267 amino acids.

The macroclass AB8 has a sequence of beta strands alternating with alpha helices or long loops with a large standard deviation on the lengths of the beta strands. There are 7, 8 or 9 such repeats. Twenty four DSMs have been constructed to cover the domain length range from 196 to 365 amino acids.

The macroclass AB8BL has a sequence of exactly eight repeats of an "alpha-beta plex." An alpha-beta plex consists of the sequence (beta strand)-(turn or loop)-(amphipathic alpha helix), with a small probability of the helix being replaced by a short helix plus a loop. The lengths of the beta strands are constrained to be of nearly identical length. The helices and/or connecting loops are constrained to contain at least 1.8 times the number of amino acids as the beta strands. Eight DSMs have been constructed to cover the domain length range from 169 to 391 amino acids. This is one of the most constrained of our macroclasses and is overlapped to some degree by AB8.

The macroclass DAB has larger standard deviations (compared to other alpha-beta macroclasses) on both the lengths of the strands and their number. Also, there are fewer constraints on the connecting helices, loops, and loops-plus-turns as compared to AB5, AB8, and AB8BL. In DAB, each strand and each helix may be either exposed to the solvent or buried. This model is designed to cover the more variable alpha-beta domains for which AB5, AB8, and AB8BL are too constrained. Six DSMs have been constructed to cover the domain length range from 115 to 600 amino acids.

The macroclass IR is composed of beta hairpins, loops, and short amphipathic alpha helices. Four DSMs have been constructed to cover the domain length range from 53 to 132 amino acids.

The macroclass IRA is composed only of loops and short amphipathic alpha helices. Four DSMs have been constructed to cover the domain length range from 48 to 116 amino acids.

The macroclass IRLS is composed of only of loops, turns, and beta strands, with the probability of a beta hairpin (strand-turn-strand) being 0.5. Four DSMs have been constructed to cover the domain length range from 37 to 112 amino acids.

The macroclass IRLT is composed of loops and beta turns. The amino-acid composition is such that 15% of the loops are cysteine or histidine residues. Four DSMs have been constructed to cover the domain length range from 30 to 86 amino acids.