FlexX-Scan: fast, structure-based virtual screening

Proteins
Ingo Schellhammer, Matthias Rarey

Abstract

We present a new software module, FlexX-Scan, for high-throughput, structure-based virtual screening. FlexX-Scan was developed with the aim to further speed up the virtual screening process. Based on the incremental construction docking tool FlexX (Rarey et al., J Mol Biol 1996;261:470-489), a compact descriptor for representing favorable protein interaction spots within the protein binding site has been developed. The descriptor is calculated using special-purpose clustering techniques applied to the usual interaction points created by FlexX. The algorithm automatically detects a small set of interaction spots in the binding site for positioning ligand functional groups. The parametrizations of the base placement and incremental construction algorithms have been adapted to the new interaction model. We tested the software tool on a diverse set of 200 protein-ligand complexes from the protein database (PDB) (Kramer et al., Proteins 1999;37:228-241). On average, the algorithm proposes about 90 interaction spots per binding site compared to about 1000 interaction dots in FlexX. We observe that the docking solutions of FlexX-Scan have a root-mean-square deviation from the crystal structure similar to the deviation of docking solut...Continue Reading

References

Dec 1, 1992·Journal of Computer-aided Molecular Design·H J Böhm
Feb 1, 1992·Journal of Computer-aided Molecular Design·H J Böhm
Feb 1, 1995·Journal of Computer-aided Molecular Design·A C GoodI D Kuntz
Aug 23, 1996·Journal of Molecular Biology·M RareyG Klebe
Mar 10, 1998·Journal of Computer-aided Molecular Design·I J BrunoM L Verdonk
May 6, 1998·Protein Science : a Publication of the Protein Society·D M Lorber, B K Shoichet
Jan 8, 1999·Journal of Computer-aided Molecular Design·M ViethC L Brooks
Jan 8, 1999·Journal of Computer-aided Molecular Design·Y SunI D Kuntz
Jun 17, 1999·Journal of Molecular Biology·M L VerdonkR Taylor
Apr 13, 2000·Journal of Chemical Information and Computer Sciences·X Wang, J T Wang
May 1, 2001·Journal of Molecular Biology·H ClaussenT Lengauer
Jul 27, 2001·Current Opinion in Chemical Biology·R Abagyan, M Totrov
Aug 22, 2002·Journal of Computer-aided Molecular Design·Sally A HindleThomas Lengaue
Jan 28, 2003·Drug Discovery Today·Paul D Lyne
Mar 15, 2003·Journal of Molecular Modeling·Tanja Schulz-Gasch, Martin Stahl
Mar 26, 2003·Journal of Chemical Information and Computer Sciences·Valerie J GilletJohn Bradshaw
Mar 26, 2003·Journal of Chemical Information and Computer Sciences·Edward J BarkerJeff Morris
Mar 28, 2003·Proteins·Diane Joseph-McCarthyJuan C Alvarez
Jun 27, 2003·Journal of Computer-aided Molecular Design·Maria I ZavodszkyLeslie A Kuhn
Dec 12, 2003·Journal of Medicinal Chemistry·Randy J ZauharWilliam J Welsh
Dec 30, 2003·Journal of Medicinal Chemistry·Wely B FlorianoWilliam A Goddard
Feb 14, 2006·Current Drug Discovery Technologies·Holger ClaussenChristian Lemmen

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Citations

Feb 13, 2007·Journal of Computer-aided Molecular Design·Ingo Schellhammer, Matthias Rarey
Feb 13, 2016·Parasitology·Karina P De Sousa, Denise L Doolan
Jun 17, 2006·Journal of Molecular Graphics & Modelling·Yoshifumi FukunishiHaruki Nakamura
Jul 23, 2013·Biophysical Journal·Rebecca J SwettAndrew L Feig
May 31, 2015·Biotechnology Advances·Pakornwit SarnpitakAndreas Hofmann
Jun 16, 2016·Medicinal Research Reviews·Agostinho LemosMaria Emília Sousa
Dec 14, 2011·Journal of Chemical Information and Modeling·Andrea VolkamerMatthias Rarey
Mar 14, 2011·Molecular Informatics·Thomas LemckeConrad Kunick
Nov 1, 2016·Expert Opinion on Drug Discovery·Joungmok KimJoohun Ha
Jan 28, 2015·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Bruno J NevesPedro V L Cravo
Nov 15, 2017·Scientific Reports·Nafisa M HassanChee-Keong Kwoh
May 15, 2018·Expert Opinion on Therapeutic Patents·Vincenza AndrisanoManuela Bartolini
Oct 7, 2016·The Open Medicinal Chemistry Journal·David Ramírez
Jul 26, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Gnanendra ShanmugamJunhyun Jeon
Dec 26, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Yuan LiuZhiqiang Wang
Mar 17, 2019·International Journal of Environmental Research and Public Health·Syed Awais AttiqueMuhammad Zohaib Nawaz
Jan 10, 2019·BMC Pharmacology & Toxicology·Limeng PuMichal Brylinski
Apr 24, 2020·Scientific Reports·Aman Chandra KaushikDong-Qing Wei
Jan 2, 2008·Journal of Chemical Information and Modeling·Yoshifumi Fukunishi, Haruki Nakamura
Sep 26, 2006·Journal of Chemical Information and Modeling·Yoshifumi FukunishiHaruki Nakamura
Jul 25, 2021·International Journal of Molecular Sciences·Sayi'Mone Tati, Laleh Alisaraie
Apr 10, 2009·Journal of Chemical Information and Modeling·Jochen Schlosser, Matthias Rarey
Apr 6, 2005·Journal of Chemical Information and Modeling·Markus H J Seifert
Sep 25, 2010·ACS Chemical Biology·Sanofar J AbdeenAndrew L Feig
Sep 15, 2017·The Journal of Physical Chemistry. B·Maria G KhrenovaAlexander V Nemukhin
Sep 16, 2005·Journal of Medicinal Chemistry·Maria A MitevaBruno O Villoutreix
Oct 9, 2021·Briefings in Bioinformatics·Qiaoming LiuGuohua Wang

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