Relationship between protein structure and geometrical constraints

Ole Lund, Jan Hansen, Søren Brunak, Jakob Bohr

Research output: Contribution to journalJournal articleResearchpeer-review


We evaluate to what extent the structure of proteins can be deduced from incomplete knowledge of disulfide bridges, surface assignments, secondary structure assignments, and additional distance constraints. A cost function taking such constraints into account was used to obtain protein structures using a simple minimization algorithm. For small proteins, the approximate structure could be obtained using one additional distance constraint for each amino acid in the protein. We also studied the effect of using predicted secondary structure and surface assignments. The constraints used in this approach typically may be obtained from low-resolution experimental data. When using a cost function based on distances, half of the resulting structures will be mirrored, because the resulting structure and its mirror image will have the same cost. The secondary structure assignments were therefore divided into chirality constraints and distance constraints. Here we report that the problem of mirrored structures, in some cases, can be solved by using a chirality term in the cost function.
Original languageEnglish
JournalProtein Science
Issue number11
Pages (from-to)2217-2225
Publication statusPublished - 1996


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