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Databases/Programmes

Scientific servers at the Institute of Enzymology

Various bioinformatics servers developed by the Research Groups of the Institute of Enzymology dealing with DNA and amino acid sequences of proteins as well as structures of globular and transmembrane proteins. The servers and their descriptions can be accessed via the following link:

http://www.enzim.hu/index.php?option=com_content&task=blogcategory&id=30&Itemid=92

MisPred

MisPred is a resource for identification of erroneous protein sequences in public databases.

http://www.mispred.com/

FixPred

FixPred is a resource for for correction of erroneous protein sequences.

http://www.fixpred.com/

Databases at the Institute of Enzymology

Transmembrane structure and topology databases developed by the Protein Structure Research Group of the Institute of Enzymology. The databases and their descriptions can be accessed via the following link:

http://www.enzim.hu/index.php?option=com_content&task=blogcategory&id=31&Itemid=93

MisPred

MisPred is a resource for identification of erroneous protein sequences in public databases.

http://www.mispred.com/

FixPred

FixPred is a resource for for correction of erroneous protein sequences.

http://www.fixpred.com/


Quantum chemical programs

István Mayer’s personal professional website which contains free available quantum chemical programs, advanced teaching textbooks and list of publications.

http://occam.chemres.hu


MassKinetics

Theory and Windows-based program to calculate mass spectra. For research and for teaching mass spectrometry and reaction kinetics.

http://www.chemres.hu/ms/masskinetics/

GlycoMiner

Computer software to determine the N-glycosylation of proteins from glycopeptide LC-MS/MS measurements.

http://www.chemres.hu/ms/glycominer/

X-ray Photoelectron Spectroscopy

XPS MultiQuant is a quantitative evaluation program for X-ray Photoelectron Spectroscopy, serving as a practical and universal tool for the surface spectroscopist. It applies the “classic” methods of quantitative calculations using the integrated intensity of the measured XPS lines.

XMQhome


Computer code for method and model comparison (ranking and grouping, as well).

VBA program’s homepage

Sum of (abolute) ranking differences (SRD) and its validation:

Compare Ranks with Random Numbers (CRRN ) without ties.

Authors: Dr. Klára Kollár-Hunek and Dr. Károly Héberger

email: kollarne[at]mail.bme.hu and heberger.karoly[at]ttk.mta.hu

Downloadable program, samples for input and output files:

CRRN_DNA_V8_restN.xls program file

Basic input file sample: Basic_DataSample.xls

Output of basic input file: Basic_DataSample_DNA_V6_CRRN.xls

Special input file sample: DataSample_Freq2.xls

Output of special input file: DataSample_Freq2_DNA_V6_CRRN.xls

For MATLAB code to perform sum of ranking differences (SRD)visit:

http://www.isu.edu/chem/people/faculty/kalijohn/

(see at the end of the page: 2013_12_16_SRD.zip)


“SRD with ties: SRDrep_V5_E10.xlsm program file

1.input sample (xls file with several sheets)  ;   Output of the 1.input file

2.input sample (xlsx file with one sheet)  ;   Output of the 2.input file

Warning: The SRD-with-ties program is for Excel-2010, and needs Solver among the VBA Tools (References)

Coming soon: SRD-with-ties program which doesn’t need the Solver.

If you have problems with using Solver in Excel, then wait for the new program version,

where we build in a new approximation of the SRD-with-ties probability distribution.

Here you see, how you can check after opening the downloaded SRDrep_V5_E10.xlsm program

whether you have the Solver among the VBA Tools (References):

For MATLAB code to perform sum of ranking differences (SRD)visit:

http://www.isu.edu/chem/people/faculty/kalijohn/

(see at the end of the page: 2013_12_16_SRD.zip)”


Generalization of the Pair-correlation Method (GPCM) – a VBA code for variable (feature) selection,

PCM works in MS Excel 97-2003 version: PCM.xla

Input file: PCM_McReynolds.xls

Output file (example for Williams t-test): PCM_McReynoldsResults.xls

Program usage,  options and explanations can be found in the references (below).

The program is downloadable freely, provided proper references are cited as shown below:

PCM distinction between two variables X1 and X2 (using one dependent variable (supervisor) Y) :

Róbert Rajkó, and Károly Héberger, Conditional Fisher’s exact test as a selection criterion for pair-correlation method. Type I and Type II errors

Chemometrics and Intelligent Laboratory Systems, 57 (2001) 1-14.

Generalization of PCM (GPCM) for more independent  (X) variables:

Károly Héberger and Róbert Rajkó: Generalization of Pair-Correlation Method (PCM) for Nonparametric Variable Selection

Journal of Chemometrics, 16 (2002) 436-443.

GPCM application:

Károly Héberger and Róbert Rajkó: Variable Selection using Pair-Correlation Method. Environmental Applications.

SAR and QSAR in Environmental Research, 13 (2002) 541-554.

Application of GPCM for idenfication of product strengths and weaknesses in sensory and consumer sciences:

Attila Gere, László Sipos, Károly Héberger, Generalized Pairwise Correlation and method comparison: Impact assessment for JAR attributes on overall liking. Food Quality and Preference, 43 (2015) 88-96.

PCM works in MS Excel 97-2003 version: PCM.xla

PCM2 works in MS Excel 2010 version: PCM2.xlam 

Input file: PCM_McReynolds.xls

Output file (example for Williams t-test): PCM_McReynoldsResults.xls