SDM: a server for predicting effects of mutations on protein stability

Nucleic Acids Research
Arun Prasad PanduranganTom L Blundell

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.

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Citations

Mar 24, 2018·Scientific Reports·Sundeep Chaitanya VedithiTom L Blundell
May 12, 2017·Expert Opinion on Drug Discovery·Amanda T S AlbanazDavid B Ascher
May 3, 2018·Bioinformatics·Fabrizio PucciMarianne Rooman
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Oct 22, 2019·Journal of Biomolecular Structure & Dynamics·Nurul Fatin Syamimi Khairul AnuarAzzmer Azzar Abdul Hamid
Nov 7, 2019·Protein Science : a Publication of the Protein Society·Arun Prasad Pandurangan, Tom L Blundell
Jan 8, 2020·Biomolecules·Óscar Álvarez-MachancosesAndrzej Kloczkowski
Apr 14, 2020·Physical Chemistry Chemical Physics : PCCP·Bo WangJohn Z H Zhang
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May 21, 2020·Nucleic Acids Research·Yoochan MyungDavid B Ascher
Oct 31, 2019·Bioinformatics·Yoochan MyungDouglas E V Pires
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Apr 30, 2020·Biomolecules·Peder A G LillebostadPetri Kursula
Sep 23, 2020·Scientific Reports·Lukas GerasimaviciusJoseph A Marsh

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