Practical Guide to Homology Modeling: Difference between revisions
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To create a 3D homology model (also called a comparative model) for a query sequence, the first step is to find a template: a [[Quality assessment for molecular models|reliable]] empirical structure with significant sequence identity. Depending on the stringency of your sequence identity criteria, templates will be available for no more than '''~30%''' of query sequences. | To create a 3D homology model (also called a comparative model) for a query sequence, the first step is to find a template: a [[Quality assessment for molecular models|reliable]] empirical structure with significant sequence identity. Depending on the stringency of your sequence identity criteria, templates will be available for no more than '''~30%''' of query sequences. | ||
'''Full-length templates are unlikely to be found''' for larger proteins (>~200 residues). 89% of structures in the [[Protein Data Bank]] were determined by [[X-ray crystallography]]. Most crystallographic structures represent fragments of full-length proteins, because fragments generally give higher crystallization success<ref>The overall success rate for solving the 3D structure of a given protein sequence is about 5%. Failures commonly occur because the expressed protein is not sufficiently soluble (about half), because soluble proteins fail to crystallize, or because crystals are not well ordered.</ref>. 10% of structures in the Protein Data Bank were determined by solution [[NMR]], but these tend to be small proteins or single domains. The median molecular mass of structures determined by NMR is 10 KD<ref name="mmm">Median molecular masses in the PDB were determined in December, 2014.</ref> (about 90 amino acids<ref>The average mass of an amino acid is 111.4 Daltons, weighted according to the frequencies of occurrences in proteins.</ref>). NMR is generally not able to determine atomic resolution structures for proteins >30 KD | '''Full-length templates are unlikely to be found''' for larger proteins (>~200 residues). 89% of structures in the [[Protein Data Bank]] were determined by [[X-ray crystallography]]. Most crystallographic structures represent fragments of full-length proteins, because fragments generally give higher crystallization success<ref>The overall success rate for solving the 3D structure of a given protein sequence is about 5%. Failures commonly occur because the expressed protein is not sufficiently soluble (about half of expressed sequences), because soluble proteins fail to crystallize, or because crystals are not well ordered.</ref>. 10% of structures in the Protein Data Bank were determined by solution [[NMR]], but these tend to be small proteins or single domains. The median molecular mass of structures determined by NMR is 10 KD<ref name="mmm">Median molecular masses in the PDB were determined in December, 2014.</ref> (about 90 amino acids<ref>The average mass of an amino acid is 111.4 Daltons, weighted according to the frequencies of occurrences in proteins.</ref>). NMR is generally not able to determine atomic resolution structures for proteins >30 KD. | ||
In contrast, the median molecular mass of [[asymmetric units]] determined by X-ray crystallography is 50 KD<ref name="mmm" />, and a few are very large, such as virus capsids (e.g. 4qyk, ~2 million Daltons; 4v99, 10 million Daltons) or ribosomes (e.g. 4w2i, 4.5 million Daltons). | |||
== References == | == References == | ||
<references/> | <references/> | ||
