Dariusz Plewczynski

Summary

Affiliation: Interdisciplinary Centre for Mathematical and Computational Modelling
Country: Poland

Publications

  1. pmc Integrated web service for improving alignment quality based on segments comparison
    Dariusz Plewczynski
    Bioinformatics Laboratory, BioInfoBank Institute, Poznan, Poland
    BMC Bioinformatics 5:98. 2004
  2. ncbi request reprint Virtual high throughput screening using combined random forest and flexible docking
    Dariusz Plewczynski
    Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawinskiego 5A, 02 106 Warsaw, Poland
    Comb Chem High Throughput Screen 12:484-9. 2009
  3. pmc AMS 4.0: consensus prediction of post-translational modifications in protein sequences
    Dariusz Plewczynski
    Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, 5a Street, 02 106 Warsaw, Poland
    Amino Acids 43:573-82. 2012
  4. pmc AMS 3.0: prediction of post-translational modifications
    Subhadip Basu
    Department of Computer Science and Engineering, Jadavpur University, Kolkata 700032, India
    BMC Bioinformatics 11:210. 2010
  5. doi request reprint The interactome: predicting the protein-protein interactions in cells
    Dariusz Plewczynski
    Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawinskiego 5A, 02 106 Warsaw, Poland
    Cell Mol Biol Lett 14:1-22. 2009
  6. ncbi request reprint AutoMotif Server for prediction of phosphorylation sites in proteins using support vector machine: 2007 update
    Dariusz Plewczynski
    Interdisciplinary Centre for Mathematical and Computational Modeling, University of Warsaw, Pawinskiego 5A, 02 106, Warsaw, Poland
    J Mol Model 14:69-76. 2008
  7. ncbi request reprint In silico prediction of SARS protease inhibitors by virtual high throughput screening
    Dariusz Plewczynski
    Interdisciplinary Centre for Mathematical and Computational Modeling, University of Warsaw, Pawinskiego 5a Street, 02 106 Warsaw, Poland
    Chem Biol Drug Des 69:269-79. 2007
  8. doi request reprint Meta-basic estimates the size of druggable human genome
    Dariusz Plewczynski
    Interdisciplinary Centre for Mathematical and Computational Modeling, University of Warsaw, Pawinskiego 5A, 02 106 Warsaw, Poland
    J Mol Model 15:695-9. 2009
  9. doi request reprint kNNsim: k-nearest neighbors similarity with genetic algorithm features optimization enhances the prediction of activity classes for small molecules
    Dariusz Plewczynski
    Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawinskiego 5A, 02 106 Warsaw, Poland
    J Mol Model 15:591-6. 2009
  10. ncbi request reprint Prediction of signal peptides in protein sequences by neural networks
    Dariusz Plewczynski
    Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Warszawa, Poland
    Acta Biochim Pol 55:261-7. 2008

Collaborators

Detail Information

Publications34

  1. pmc Integrated web service for improving alignment quality based on segments comparison
    Dariusz Plewczynski
    Bioinformatics Laboratory, BioInfoBank Institute, Poznan, Poland
    BMC Bioinformatics 5:98. 2004
    ..Structural comparison is able to detect approximately twice as many distant relationships as sequence comparison at the same error rate...
  2. ncbi request reprint Virtual high throughput screening using combined random forest and flexible docking
    Dariusz Plewczynski
    Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawinskiego 5A, 02 106 Warsaw, Poland
    Comb Chem High Throughput Screen 12:484-9. 2009
    ....
  3. pmc AMS 4.0: consensus prediction of post-translational modifications in protein sequences
    Dariusz Plewczynski
    Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, 5a Street, 02 106 Warsaw, Poland
    Amino Acids 43:573-82. 2012
    ..The source code and precompiled binaries of brainstorming tool are available at http://code.google.com/p/automotifserver/ under Apache 2.0 licensing...
  4. pmc AMS 3.0: prediction of post-translational modifications
    Subhadip Basu
    Department of Computer Science and Engineering, Jadavpur University, Kolkata 700032, India
    BMC Bioinformatics 11:210. 2010
    ..The database of sequence segments with confirmed by experiments post-translational modification sites are used for training a set of ANNs...
  5. doi request reprint The interactome: predicting the protein-protein interactions in cells
    Dariusz Plewczynski
    Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawinskiego 5A, 02 106 Warsaw, Poland
    Cell Mol Biol Lett 14:1-22. 2009
    ..The proposed validation of the theoretical methods using experimental data would be a better assessment of their accuracy...
  6. ncbi request reprint AutoMotif Server for prediction of phosphorylation sites in proteins using support vector machine: 2007 update
    Dariusz Plewczynski
    Interdisciplinary Centre for Mathematical and Computational Modeling, University of Warsaw, Pawinskiego 5A, 02 106, Warsaw, Poland
    J Mol Model 14:69-76. 2008
    ..bioinfo.pl/ . Additionally, the reference dataset for optimization of prediction of phosphorylation sites, collected from the UniProtKB was also provided and can be accessed at http://ams2.bioinfo.pl/data/ ...
  7. ncbi request reprint In silico prediction of SARS protease inhibitors by virtual high throughput screening
    Dariusz Plewczynski
    Interdisciplinary Centre for Mathematical and Computational Modeling, University of Warsaw, Pawinskiego 5a Street, 02 106 Warsaw, Poland
    Chem Biol Drug Des 69:269-79. 2007
    ..Selected molecules having close structural relationship to a 2-methyl-2,4-pentanediol may provide candidate lead compounds toward the development of novel allosteric severe acute respiratory syndrome protease inhibitors...
  8. doi request reprint Meta-basic estimates the size of druggable human genome
    Dariusz Plewczynski
    Interdisciplinary Centre for Mathematical and Computational Modeling, University of Warsaw, Pawinskiego 5A, 02 106 Warsaw, Poland
    J Mol Model 15:695-9. 2009
    ....
  9. doi request reprint kNNsim: k-nearest neighbors similarity with genetic algorithm features optimization enhances the prediction of activity classes for small molecules
    Dariusz Plewczynski
    Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawinskiego 5A, 02 106 Warsaw, Poland
    J Mol Model 15:591-6. 2009
    ..As a consequence, the method can be easily applied to large commercial compounds collections in a drug development campaign in order to significantly reduce the number of ligands for further costly experimental validation...
  10. ncbi request reprint Prediction of signal peptides in protein sequences by neural networks
    Dariusz Plewczynski
    Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Warszawa, Poland
    Acta Biochim Pol 55:261-7. 2008
    ..As a consequence, the method can be easily applied to genome-wide datasets. The software can be downloaded freely from http://rpsp.bioinfo.pl/RPSP.tar.gz...
  11. pmc Brainstorming: weighted voting prediction of inhibitors for protein targets
    Dariusz Plewczynski
    Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawinskiego 5a Street, 02 106, Warsaw, Poland
    J Mol Model 17:2133-41. 2011
    ..Depending on the protein target, the overall recall value is raised by at least 20% in comparison to any single machine learning method (including ensemble methods like random forest) and unweighted simple majority voting procedures...
  12. doi request reprint VoteDock: consensus docking method for prediction of protein-ligand interactions
    Dariusz Plewczynski
    Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawinskiego 5a Street, 02 106 Warsaw, Poland
    J Comput Chem 32:568-81. 2011
    ..5 Å. Finally, we were able to increase the Pearson correlation of the predicted binding affinity in comparison with the experimental value up to 0.5...
  13. ncbi request reprint Comparison of proteins based on segments structural similarity
    Dariusz Plewczynski
    Interdisciplinary Center for Mathematical and Computational Modeling Warsaw University, Warszawa, Poland
    Acta Biochim Pol 51:161-72. 2004
    ..bioinfo.pl/ free for academic use, with a weekly updated database containing a set of 5000 structures from the Protein Data Bank with non-homologous sequences...
  14. pmc PSP_MCSVM: brainstorming consensus prediction of protein secondary structures using two-stage multiclass support vector machines
    Piyali Chatterjee
    Department of Computer Science and Engineering, Netaji Subhash Engineering College, Garia, Kolkata, 700152, India
    J Mol Model 17:2191-201. 2011
    ..PSP_MCSVM source code, train-test datasets and supplementary files are available freely in public domain at: http://sysbio.icm.edu.pl/secstruct and http://code.google.com/p/cmater-bioinfo/..
  15. doi request reprint Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database
    Dariusz Plewczynski
    Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawinskiego 5a Street, 02 106 Warsaw, Poland
    J Comput Chem 32:742-55. 2011
    ....
  16. ncbi request reprint Performance of machine learning methods for ligand-based virtual screening
    Dariusz Plewczynski
    Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawinskiego 5a Street, Warsaw, Poland
    Comb Chem High Throughput Screen 12:358-68. 2009
    ....
  17. pmc Consensus classification of human leukocyte antigen class II proteins
    Indrajit Saha
    Interdisciplinary Centre for Mathematical and Computational Modeling, University of Warsaw, Warsaw, Poland
    Immunogenetics 65:97-105. 2013
    ..icm.edu.pl/HLA ...
  18. pmc Fuzzy clustering of physicochemical and biochemical properties of amino acids
    Indrajit Saha
    Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, 02 106 Warsaw, Poland
    Amino Acids 43:583-94. 2012
    ..The processed AAindex1 database, supplementary material and the software are available at http://sysbio.icm.edu.pl/aaindex/ ...
  19. doi request reprint Protein-protein interaction and pathway databases, a graphical review
    Tomas Klingström
    Uppsala University
    Brief Bioinform 12:702-13. 2011
    ..pathguide.org and can be accessed at http://www.pathguide.org/interactions.php in a new Cytoscape web implementation. The local copy of Cytoscape cys file can be downloaded from http://bio.icm.edu.pl/~darman/ppi web page...
  20. ncbi request reprint 3D-Hit: fast structural comparison of proteins
    Dariusz Plewczynski
    Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Warsaw, Poland
    Appl Bioinformatics 1:223-5. 2002
    ..These initial hits are expanded by two iterations of structural superposition of larger segments of 99 and 299 residues. The method generates an alignment for the query protein by concatenating partial structural alignments...
  21. doi request reprint PPI_SVM: prediction of protein-protein interactions using machine learning, domain-domain affinities and frequency tables
    Piyali Chatterjee
    Department of Computer Science and Engineering, Netaji Subhash Engineering College, Garia, Kolkata, 700152, India
    Cell Mol Biol Lett 16:264-78. 2011
    ..The PPI_SVM source code, train/test datasets and supplementary files are available freely in the public domain at: http://code.google.com/p/cmater-bioinfo/...
  22. ncbi request reprint Support-vector-machine classification of linear functional motifs in proteins
    Dariusz Plewczynski
    BioInfoBank Institute, Limanowskiego 24A 16, 60 744, Poznan, Poland
    J Mol Model 12:453-61. 2006
    ..The resulting list of plausible post-translational sites in the query protein is returned to the user. We also present a study of the human protein kinase C family as a biological application of our method...
  23. doi request reprint HarmonyDOCK: the structural analysis of poses in protein-ligand docking
    Dariusz Plewczynski
    1 Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Warsaw, Poland
    J Comput Biol 21:247-56. 2014
    ..We found out that some docking programs perform considerably better than the others, yet in all cases the proper selection of decoys, namely HarmonyDOCK, is needed for successful docking procedure...
  24. doi request reprint Ensemble learning prediction of protein-protein interactions using proteins functional annotations
    Indrajit Saha
    Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Warsaw, Poland
    Mol Biosyst 10:820-30. 2014
    ..These results confirmed that our datasets are suitable for performing PPI prediction and Ensemble Learning method is well suited for this task. Both the processed PPI datasets and the software are available at . ..
  25. doi request reprint GIDMP: good protein-protein interaction data metamining practice
    Dariusz Plewczynski
    Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, ul Pawinskiego 5a, 02 106, Warsaw, Poland
    Cell Mol Biol Lett 16:258-63. 2011
    ..The proposed information can be presented as a few hidden lines of text on the source database www page, and a constantly updated table for a metamining database included in the source/credits web page...
  26. ncbi request reprint Improved differential evolution for microarray analysis
    Indrajit Saha
    Interdisciplinary Centre for Mathematical and Computational Modeling ICM, University of Warsaw, Al Zwirki i Wigury 93, floor 2 1 2, 02 089 Warsaw, Poland
    Int J Data Min Bioinform 6:86-103. 2012
    ..Statistical and biological significance tests have been carried out to establish the statistical superiority of the proposed clustering approach and biological relevance of clusters of co-expressed genes, respectively...
  27. ncbi request reprint AutoMotif server: prediction of single residue post-translational modifications in proteins
    Dariusz Plewczynski
    BioInfoBank Institute, Limanowskiego 24A 16, 60 744 Poznan, Poland
    Bioinformatics 21:2525-7. 2005
    ..The accuracy of the identification is estimated using the standard leave-one-out procedure. The sensitivities for all types of short LFMs are in the range of 70%...
  28. doi request reprint Using Dali for structural comparison of proteins
    Liisa Holm
    Institute of Biotechnology, University of Helsinki, Helsinki, Finland
    Curr Protoc Bioinformatics . 2006
    ..All Dali resources use an identical algorithm for structure comparison. Users may run Dali using the Web, or the program may be downloaded to be run locally on Linux computers...
  29. pmc PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics
    Marcin von Grotthuss
    Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
    BMC Bioinformatics 7:53. 2006
    ..Many of these structures are functionally unannotated because they have no sequence similarity to proteins of known function. However, it is possible to successfully infer function using only structural similarity...
  30. ncbi request reprint Molecular modeling of phosphorylation sites in proteins using a database of local structure segments
    Dariusz Plewczynski
    BioInfoBank Institute, Limanowskiego 24A 16, 60 744 Poznan, Poland
    J Mol Model 11:431-8. 2005
    ....
  31. ncbi request reprint Target specific compound identification using a support vector machine
    Dariusz Plewczynski
    BioInfoBank Institute, Limanowskiego 24A 16, 60 744 Poznan, Poland
    Comb Chem High Throughput Screen 10:189-96. 2007
    ..The subsequent use of our machine learning method was found to improve the speed (since the docking procedure was not required for all compounds from the database) and also the accuracy of the HTS hit lists (the enrichment factor)...
  32. pmc 3D-Fun: predicting enzyme function from structure
    Marcin von Grotthuss
    CMBI, NCMLS, Radboud University Nijmegen Medical Centre, Geert Grooteplein 26 28, 6525 GA Nijmegen, The Netherlands
    Nucleic Acids Res 36:W303-7. 2008
    ..Currently, the 3D-Fun system only predicts enzyme function but an expanded version with Gene Ontology predictions will be available soon. The server can be accessed at http://3dfun.bioinfo.pl/ or at http://3dfun.cmbi.ru.nl/...
  33. ncbi request reprint Uncharacterized DUF1574 leptospira proteins are SGNH hydrolases
    Lukasz Knizewski
    Cell Cycle 7:542-4. 2008
  34. ncbi request reprint Assessing different classification methods for virtual screening
    Dariusz Plewczynski
    BioInfoBank Institute, Limanowskiego 24A 16, 60 744 Poznan, Poland
    J Chem Inf Model 46:1098-106. 2006
    ....