Homology modeling servers: Difference between revisions
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<nowiki>**</nowiki>Covalent peptide bonds between amino acids are not explicit in [[PDB files]], but all commonly used software places covalent bonds based on interatomic distances. Thus, when a spatial gap is omitted in the 3D model, the two residues abutting the gap are effectively ligated. | <nowiki>**</nowiki>Covalent peptide bonds between amino acids are not explicit in [[PDB files]], but all commonly used software places covalent bonds based on interatomic distances. Thus, when a spatial gap is omitted in the 3D model, the two residues abutting the gap are effectively ligated. | ||
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<nowiki>***</nowiki>In the case examined, segments of the | <nowiki>***</nowiki>In the case examined, segments of the template sequence were missing from the sequence alignment for no apparent reason. | ||
==Problems== | ==Problems== | ||
