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Detecting distant homology with Meta-BASIC.
Ginalski K, von Grotthuss M, Grishin NV, Rychlewski L. Ginalski K, et al. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W576-81. doi: 10.1093/nar/gkh370. Nucleic Acids Res. 2004. PMID: 15215454 Free PMC article.
3D-Fun: predicting enzyme function from structure.
von Grotthuss M, Plewczynski D, Vriend G, Rychlewski L. von Grotthuss M, et al. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W303-7. doi: 10.1093/nar/gkn308. Epub 2008 May 30. Nucleic Acids Res. 2008. PMID: 18515349 Free PMC article.
3D-Hit: fast structural comparison of proteins.
Plewczyński D, Paś J, von Grotthuss M, Rychlewski L. Plewczyński D, et al. Appl Bioinformatics. 2002;1(4):223-5. Appl Bioinformatics. 2002. PMID: 15130838
Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors.
Hoffmann M, Eitner K, von Grotthuss M, Rychlewski L, Banachowicz E, Grabarkiewicz T, Szkoda T, Kolinski A. Hoffmann M, et al. J Comput Aided Mol Des. 2006 May;20(5):305-19. doi: 10.1007/s10822-006-9057-z. Epub 2006 Sep 14. J Comput Aided Mol Des. 2006. PMID: 16972168 Free PMC article.
Structure prediction, evolution and ligand interaction of CHASE domain.
Pas J, von Grotthuss M, Wyrwicz LS, Rychlewski L, Barciszewski J. Pas J, et al. FEBS Lett. 2004 Oct 22;576(3):287-90. doi: 10.1016/j.febslet.2004.09.020. FEBS Lett. 2004. PMID: 15498549
Comparison of proteins based on segments structural similarity.
Plewczynski D, Pas J, Von Grotthuss M, Rychlewski L. Plewczynski D, et al. Acta Biochim Pol. 2004;51(1):161-72. Acta Biochim Pol. 2004. PMID: 15094837 Review.
Ligand-Info, searching for similar small compounds using index profiles.
von Grotthuss M, Pas J, Rychlewski L. von Grotthuss M, et al. Bioinformatics. 2003 May 22;19(8):1041-2. doi: 10.1093/bioinformatics/btg117. Bioinformatics. 2003. PMID: 12761071
ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure.
Ginalski K, Pas J, Wyrwicz LS, von Grotthuss M, Bujnicki JM, Rychlewski L. Ginalski K, et al. Nucleic Acids Res. 2003 Jul 1;31(13):3804-7. doi: 10.1093/nar/gkg504. Nucleic Acids Res. 2003. PMID: 12824423 Free PMC article.
VoteDock: consensus docking method for prediction of protein-ligand interactions.
Plewczynski D, Łaźniewski M, von Grotthuss M, Rychlewski L, Ginalski K. Plewczynski D, et al. J Comput Chem. 2011 Mar;32(4):568-81. doi: 10.1002/jcc.21642. Epub 2010 Sep 1. J Comput Chem. 2011. PMID: 20812324 Free PMC article.
PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics.
von Grotthuss M, Plewczynski D, Ginalski K, Rychlewski L, Shakhnovich EI. von Grotthuss M, et al. BMC Bioinformatics. 2006 Feb 6;7:53. doi: 10.1186/1471-2105-7-53. BMC Bioinformatics. 2006. PMID: 16460560 Free PMC article.
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