ArticleNucleic acids research2017
SDM: a server for predicting effects of mutations on protein stability.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 263 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
263 citing papers in PubMed, 528 citations in OpenAlex.
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- A Campomelic Dysplasia A76E Mutation in Sox9 Destabilizes Protein and DNA Binding Dynamics.Biomolecules · 2026Article
- In silico structural and functional characterization of high-risk missense variants in MMP8, GZMK, and OASL genes associated with epidemic viral infections.Scientific reports · 2026Article
- Genome-wide analyses of Mycobacterium tuberculosis complex isolates reveal insights into circulating lineages and drug resistance mutations in The Gambia.Scientific reports · 2026Article
- Computational identification of rare pathogenic genomic variants in esophageal cancer markers: Transcript-level analysis, sequence-based insights, and structural-functional impacts of non-synonymous SNPs.Biochemistry and biophysics reports · 2026Article
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- Mapping the Functional Epitopes of Human Growth Hormone: Integrating Structural and Evolutionary Data with Clinical Variants.Current issues in molecular biology · 2025Article
- Bioinformatics-driven identification of pathogenic missense nsSNPs in the human proto-oncogene SRC and cancer susceptibility.Journal, genetic engineering & biotechnology · 2025Article
- Identification of deleterious non-synonymous single nucleotide polymorphisms in the mRNA decay activator ZFP36L2.RNA biology · 2025Article
- DDGWizard: Integration of feature calculation resources for analysis and prediction of changes in protein thermostability upon point mutations.PLoS computational biology · 2025Article
- Engineering of Nocardioides acrostichi lipase: utilizing natural variation and mutational free energy to alter expression and functional properties.Journal of biological engineering · 2025Article
- Integrative structural profiling and ligand optimisation across the transthyretin mutational landscape.NPJ systems biology and applications · 2025Article
- Association Between FABP3 and FABP4 Genes with Changes in Milk Composition and Fatty Acid Profiles in the Native Southern Yellow Cattle Breed.Veterinary sciences · 2025Article
- A pro-angiogenic and hypoxic zebrafish model as a novel platform for anti-angiogenic drug testing.Biology open · 2025Article
203 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.