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Publications for ProNIT
Mapping genetic variations to three dimensional protein structures to enhance variant interpretation: a proposed framework
[…] m wild-type and mutant protein pairs, often using protein stability data from the ProTherm database , protein–protein binding affinities from SKEMPI , protein–nucleic acid binding affinities from ProNIT , and protein–ligand binding affinities from Platinum .A second set of methods [, , , –] predicts the phenotypic effect (pathogenicity) of mutations, most often as a binary classification: […]
Functional Annotation of Putative Regulatory Elements at Cancer Susceptibility Loci
[…] f annotating specific variants for functional effect. Similarly, nonsynonymous SNPs (nsSNPs) can be assigned function based on their impact on structural stability through databases like ProTherm and ProNit. In contrast, noncoding SNP annotations are constrained by a dearth of knowledge pertaining to the phenotypic impact of regulatory variation. However, the number of genome annotations relevant […]
Using protein design algorithms to understand the molecular basis of disease caused by protein–DNA interactions: the Pax6 example
[…] mutations in the interface with DNA and the other made of wild-type proteins interacting with different DNA sequences.The set of protein mutants in protein–DNA complexes was initially taken from the ProNIT database (). However, due to internal inconsistencies of the database, the actual data (physical data of the experiments and the change in interaction energy due to the mutation, ΔΔGint) were t […]
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