LUpsb_logo1

Protein Structure and
Bioinformatics Group

Prof. Mauno Vihinen

Lund University

Bioinformatics services

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B Cell proteome
Web site for proteomics studies of B cell differentiation.
http://structure.bmc.lu.se/BcellProteome/

 

Bioinformatics benchmarks
Benchmark datasets available in bioinformatics. Collected by Lund University Protein Structure and Bioinformatics Group (LU PSB).
http://structure.bmc.lu.se/benchmark_datasets/index.php

MultiDisp_logo

MultiDisp
is a multiple sequence alignment visualization tool that can be used to show sequence properties in several ways. The visualization schemes include graphs for coloured and property charts, identity, similarity and divergence plots as well as visualizations based on physicochemical properties.
http://structure.bmc.lu.se//MultiDisp/index.html


PID_logo

PID classification
Systematic classification of primary immunodeficiencies based on clinical, pathological and laboratory parameters.
http://structure.bmc.lu.se/PID_classification/


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.
http://structure.bmc.lu.se/PON-BTK/


PON-P_logo

PON-P2 is a machine learning-based approach to predict the pathogenicity of amino acid substitutions.
http://structure.bmc.lu.se/PON-P2/


PON-PS_logo

PON-PS is a machine learning-based approach to predict the disease severity due to amino acid substitutions.
http://structure.bmc.lu.se/PON-PS/


PON-MMR_logo

PON-MMR2 predicts the pathogenicity of amino acid substitutions in mismatch repair (MMR) proteins (MLH1, MSH2, MSH6 and PMS2).
http://structure.bmc.lu.se/PON-MMR2/


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.
http://structure.bmc.lu.se/PON-mt-tRNA/


PON-Diso_logo

PON-Diso a machine learning based prediction method to predict changes in disorder regions contained in a protein, caused by amino acid substitutions.
http://structure.bmc.lu.se/PON-Diso/


PON-Sol_logo

PON-Sol is a two-step machine learning-based method to predict the impact of amino acid substitutions on protein solubility.
http://structure.bmc.lu.se/PON-Sol/


PPSC_logo

PPSC
Prediction of Protein Stability Changes is a structure-based method to predict the effects of missense variants on protein stability.
http://structure.bmc.lu.se/PPSC/


VariBench_logo

VariBench
is a benchmark database suite comprising variation datasets for testing and training methods for variation effect prediction.
http://structure.bmc.lu.se/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.

http://structure.bmc.lu.se/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
Bioinformatics benchmarks
MultiDisp
PID classification
PON-BTK
PON-P2
PON-PS
PON-MMR2
PON-mt-tRNA
PON-Diso
PON-Sol
ProCon
PPSC
VariBench
VariSNP

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

Research:
Group members
Publications

News from PSB:
News

Links:
Lund University
Medical Faculty
Department of Experimental Medical Science


Lund University, Sweden 2015 ©