Abstract：
:Here, we report a webserver for the improved SDM, used for predicting the effects of mutations on protein stability. As a pioneering knowledge-based approach, SDM has been highlighted as the most appropriate method to use in combination with many other approaches. We have updated the environment-specific amino-acid substitution tables based on the current expanded PDB (a 5-fold increase in information), and introduced new residue-conformation and interaction parameters, including packing density and residue depth. The updated server has been extensively tested using a benchmark containing 2690 point mutations from 132 different protein structures. The revised method correlates well against the hypothetical reverse mutations, better than comparable methods built using machine-learning approaches, highlighting the strength of our knowledge-based approach for identifying stabilising mutations. Given a PDB file (a Protein Data Bank file format containing the 3D coordinates of the protein atoms), and a point mutation, the server calculates the stability difference score between the wildtype and mutant protein. The server is available at http://structure.bioc.cam.ac.uk/sdm2.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Pandurangan AP,Ochoa-Montaño B,Ascher DB,Blundell TLdoi
10.1093/nar/gkx439subject
Has Abstractpub_date
2017-07-03 00:00:00pages
W229-W235issue
W1eissn
0305-1048issn
1362-4962pii
3835311journal_volume
45pub_type
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