Pirepred
Interpretation tool for neonatal screened genetic variants
Missense, nonsense and frameshift single nucleotide variants (SNVs) annotated in the ClinVar database are retrieved in real time and presented in the structural context of the original protein. For each variant, binary classifications (tolerated/deleterious) obtained from 15 popular predictors are shown, together with a consensus ternary classification (tolerated/uncertain/deleterious). Predictions for any single amino acid replacement arising from SNVs are also shown.
Protposer
Proposal of potentially stabilizing mutations
Protposer is a protein stabilization tool that analyses PDB files and sequence databases in search for wild type amino acid residues providing opportunities for thermostabilization. Protposer proposes a list of point mutations that are likely to increase protein stability by at least 0.5 kcal/mol. To do so, it searches for divergences from ancestral or consensus sequences, from ideal alpha-helix composition or average solvent exposure of polar or apolar residues, and for the presence of cavities, electrostatic imbalance or acidic H-bonds. Protposer finds weak spots in the structure, generates and evaluates replacements, and estimates their probability of being stabilizing, using a machine learning logistic regression model.
ProtSA
Generation of unfolded ensembles of proteins and calculation of sequence-specific solvent accessibilities in the folded and unfolded states
ProtSA generates an unfolded ensemble for your protein of interest, and calculates the average solvent accessible surface area (SASA) of each atom and residue in the ensemble. All you need to provide is the sequence of your protein. In addition, if you provide a structural model, folded SASA and differences between the folded and unfolded SASA, per atom and per residue, will be calculated.
PrionScan
Online tool and database of prion domains predicted for all publicly available proteomes
Based on amino acid propensities previously observed in prion domains experimentally tested in yeast, we have built a probabilistic model, benchmarked to handle large sequence databases, and used it to predict prion-like sequence stretches in all the proteomes available annotated in UniprotKB.
ProteinLIPS
Prediction of locally unstable segments of proteins
ProteinLIPS scans protein structures, computes packing densities and surface polarities, and predicts the locally unstable segments which are likely to be the first parts of the protein to unfold, the last parts to fold or to be involved in protein dynamics. You can query using PDB codes or keywords, e.g. if interested in a family of proteins.
T-novoMS
A combined de-novo/database-search tool for MSMS tandem spectra identification
Providing one or a list of MSMS spectra (in "dta" format), you will receive an email message with the most-likely, de-novo predicted parent peptide, the best matching peptide found in uniprot, and a measure of the reliability of the de-novo and database-search predictions.
