LUpsb_logo1

Protein Structure and
Bioinformatics Group

Prof. Mauno Vihinen

Lund University

Bioinformatics services


B Cell proteome
for proteomics studies of B cell differentiation.
link


PID_logo

PID classification
systematic classification of primary immunodeficiencies based on clinical, pathological and laboratory parameters.
link


PON-All
predicts the tolerance (pathogenicity) of amino acid substitutions in multiple species.
link


PON-BTK_logo

PON-BTK
is a method for classifying variations in the kinase domain of Bruton tyrosine kinase (BTK) related to X-linked agammaglobulinemia (XLA) to disease-causing and harmful.
link


PON-Fold_logo.jpg

PON-Fold
is is the machine learning method for folding rate predictions for amino acid substitutions.
link


PON-P_logo

PON-P2
is a machine learning-based approach to predict the pathogenicity of amino acid substitutions.
link


PON-PS_logo

PON-PS
is a machine learning-based approach to predict the disease severity due to amino acid substitutions.
link


PON-MMR_logo

PON-MMR2
predicts the pathogenicity of amino acid substitutions in mismatch repair (MMR) proteins (MLH1, MSH2, MSH6 and PMS2).
link


PON-mt-tRNA_logo

PON-mt-tRNA
is a multifactorial-probability method to predict the pathogenicity of single nucleotide substitutions in human mitochondrial tRNAs. It integrates a machine learning tool and evidence of segregation, biochemical and histochemical tests.
link


PON-Diso_logo

PON-Diso
is a machine learning based prediction method to predict changes in disorder regions contained in a protein, caused by amino acid substitutions.
link


PON-Sol_logo

PON-Sol2
is a two-step machine learning-based method to predict the impact of amino acid substitutions on protein solubility.
link


pro_tstab_logo2

ProTstab2
is a predictor for protein stability as indicated melting temperature (Tm).
link


VariBench_logo

VariBench
is a benchmark database suite comprising variation datasets for testing and training methods for variation effect prediction.
/VariBench/


VariSNP_logo

VariSNP
is a benchmark database suite comprising variation datasets that can be used for developing and testing the performance of variant effect prediction tools.

/VariSNP/
Updated 2015-03-26 by Gerard Schaafsma

Home

Databases:
IDbases
KinMutBase
SH2base
ImmunoDeficiency Resource (IDR)
Immunome Knowledge Base (IKB)
GOme

Bioinformatics services:
B-Cell Proteome
PID classification
PON-BTK
PON-All
PON-P2
PON-PS
PON-MMR2
PON-mt-tRNA
PON-Diso
PON-Fold
PON-Sol2
PON-IDR
SolAcc
ProTstab2
VariBench
VariSNP

Standards and guidelines:
VariO
MIASM
HVP Guidelines
Guidelines for prediction tools
Curating gene variant databases
HVP Country Nodes
Recommendations for LSDBs
Sanasto

Links:
Lund University
Medical Faculty
Department of Experimental Medical Science


Lund University, Sweden 2015 ©