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Results: 1 to 20 of 45

1.

A combined systems and structural modeling approach repositions antibiotics for Mycoplasma genitalium.

Kazakiewicz D, Karr JR, Langner KM, Plewczynski D.

Comput Biol Chem. 2015 Jul 30. pii: S1476-9271(15)30089-X. doi: 10.1016/j.compbiolchem.2015.07.007. [Epub ahead of print]

PMID:
26271684
2.

Multi-level machine learning prediction of protein-protein interactions in Saccharomyces cerevisiae.

Zubek J, Tatjewski M, Boniecki A, Mnich M, Basu S, Plewczynski D.

PeerJ. 2015 Jul 2;3:e1041. doi: 10.7717/peerj.1041. eCollection 2015.

3.

Binding Activity Prediction of Cyclin-Dependent Inhibitors.

Saha I, Rak B, Bhowmick SS, Maulik U, Bhattacharjee D, Koch U, Lazniewski M, Plewczynski D.

J Chem Inf Model. 2015 Jul 27;55(7):1469-82. doi: 10.1021/ci500633c. Epub 2015 Jul 10.

PMID:
26079845
4.

Application of machine learning method in genomics and proteomics.

Lin H, Chen W, Anandakrishnan R, Plewczynski D.

ScientificWorldJournal. 2015;2015:914780. doi: 10.1155/2015/914780. Epub 2015 Apr 19. No abstract available.

5.

Role of the host genetic variability in the influenza A virus susceptibility.

Arcanjo AC, Mazzocco G, de Oliveira SF, Plewczynski D, Radomski JP.

Acta Biochim Pol. 2014;61(3):403-19. Epub 2014 Sep 4. Review.

6.

Ensemble learning prediction of protein-protein interactions using proteins functional annotations.

Saha I, Zubek J, Klingström T, Forsberg S, Wikander J, Kierczak M, Maulik U, Plewczynski D.

Mol Biosyst. 2014 Apr;10(4):820-30. doi: 10.1039/c3mb70486f. Epub 2014 Jan 27.

PMID:
24469380
7.

PPIcons: identification of protein-protein interaction sites in selected organisms.

Sriwastava BK, Basu S, Maulik U, Plewczynski D.

J Mol Model. 2013 Sep;19(9):4059-70. doi: 10.1007/s00894-013-1886-9. Epub 2013 Jun 2.

8.

Consensus classification of human leukocyte antigen class II proteins.

Saha I, Mazzocco G, Plewczynski D.

Immunogenetics. 2013 Feb;65(2):97-105. doi: 10.1007/s00251-012-0665-6. Epub 2012 Nov 16. Erratum in: Immunogenetics. 2013 Apr;65(4):313.

9.

AMS 4.0: consensus prediction of post-translational modifications in protein sequences.

Plewczynski D, Basu S, Saha I.

Amino Acids. 2012 Aug;43(2):573-82. doi: 10.1007/s00726-012-1290-2. Epub 2012 May 4.

10.

Improved differential evolution for microarray analysis.

Saha I, Plewczynski D, Maulik U, Bandyopadhyay S.

Int J Data Min Bioinform. 2012;6(1):86-103.

PMID:
22479820
11.

Fuzzy clustering of physicochemical and biochemical properties of amino acids.

Saha I, Maulik U, Bandyopadhyay S, Plewczynski D.

Amino Acids. 2012 Aug;43(2):583-94. doi: 10.1007/s00726-011-1106-9. Epub 2011 Oct 13.

12.

PSP_MCSVM: brainstorming consensus prediction of protein secondary structures using two-stage multiclass support vector machines.

Chatterjee P, Basu S, Kundu M, Nasipuri M, Plewczynski D.

J Mol Model. 2011 Sep;17(9):2191-201. doi: 10.1007/s00894-011-1102-8. Epub 2011 May 19.

13.

PPI_SVM: prediction of protein-protein interactions using machine learning, domain-domain affinities and frequency tables.

Chatterjee P, Basu S, Kundu M, Nasipuri M, Plewczynski D.

Cell Mol Biol Lett. 2011 Jun;16(2):264-78. doi: 10.2478/s11658-011-0008-x. Epub 2011 Mar 20.

PMID:
21442443
14.

GIDMP: good protein-protein interaction data metamining practice.

Plewczynski D, Klingström T.

Cell Mol Biol Lett. 2011 Jun;16(2):258-63. doi: 10.2478/s11658-011-0004-1. Epub 2011 Mar 9.

PMID:
21394448
15.

Detailed mechanism of squalene epoxidase inhibition by terbinafine.

Nowosielski M, Hoffmann M, Wyrwicz LS, Stepniak P, Plewczynski DM, Lazniewski M, Ginalski K, Rychlewski L.

J Chem Inf Model. 2011 Feb 28;51(2):455-62. doi: 10.1021/ci100403b. Epub 2011 Jan 13.

PMID:
21229992
16.

HarmonyDOCK: the structural analysis of poses in protein-ligand docking.

Plewczynski D, Philips A, Von Grotthuss M, Rychlewski L, Ginalski K.

J Comput Biol. 2014 Mar;21(3):247-56. doi: 10.1089/cmb.2009.0111. Epub 2010 Nov 20.

PMID:
21091053
17.

Brainstorming: weighted voting prediction of inhibitors for protein targets.

Plewczynski D.

J Mol Model. 2011 Sep;17(9):2133-41. doi: 10.1007/s00894-010-0854-x. Epub 2010 Sep 21.

18.

Protein-protein interaction and pathway databases, a graphical review.

Klingström T, Plewczynski D.

Brief Bioinform. 2011 Nov;12(6):702-13. doi: 10.1093/bib/bbq064. Epub 2010 Sep 17.

19.

VoteDock: consensus docking method for prediction of protein-ligand interactions.

Plewczynski D, Łaźniewski M, von Grotthuss M, Rychlewski L, Ginalski K.

J Comput Chem. 2011 Mar;32(4):568-81. doi: 10.1002/jcc.21642. Epub 2010 Sep 1.

20.

Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database.

Plewczynski D, Łaźniewski M, Augustyniak R, Ginalski K.

J Comput Chem. 2011 Mar;32(4):742-55. doi: 10.1002/jcc.21643. Epub 2010 Sep 1.

PMID:
20812323
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