PMID- 23705874
OWN - NLM
STAT- MEDLINE
DCOM- 20140117
LR  - 20130624
IS  - 1549-960X (Electronic)
IS  - 1549-9596 (Linking)
VI  - 53
IP  - 6
DP  - 2013 Jun 24
TI  - Evaluation and optimization of virtual screening workflows with DEKOIS 2.0--a 
      public library of challenging docking benchmark sets.
PG  - 1447-62
LID - 10.1021/ci400115b [doi]
AB  - The application of molecular benchmarking sets helps to assess the actual 
      performance of virtual screening (VS) workflows. To improve the efficiency of 
      structure-based VS approaches, the selection and optimization of various 
      parameters can be guided by benchmarking. With the DEKOIS 2.0 library, we aim to 
      further extend and complement the collection of publicly available decoy sets. 
      Based on BindingDB bioactivity data, we provide 81 new and structurally diverse 
      benchmark sets for a wide variety of different target classes. To ensure a 
      meaningful selection of ligands, we address several issues that can be found in 
      bioactivity data. We have improved our previously introduced DEKOIS methodology 
      with enhanced physicochemical matching, now including the consideration of 
      molecular charges, as well as a more sophisticated elimination of latent actives 
      in the decoy set (LADS). We evaluate the docking performance of Glide, GOLD, and 
      AutoDock Vina with our data sets and highlight existing challenges for VS tools. 
      All DEKOIS 2.0 benchmark sets will be made accessible at http://www.dekois.com.
FAU - Bauer, Matthias R
AU  - Bauer MR
AD  - Laboratory for Molecular Design and Pharmaceutical Biophysics, Department of 
      Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Eberhard Karls 
      University Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany.
FAU - Ibrahim, Tamer M
AU  - Ibrahim TM
FAU - Vogel, Simon M
AU  - Vogel SM
FAU - Boeckler, Frank M
AU  - Boeckler FM
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20130612
PL  - United States
TA  - J Chem Inf Model
JT  - Journal of chemical information and modeling
JID - 101230060
RN  - 0 (Proteins)
SB  - IM
MH  - *Databases, Protein
MH  - *Drug Design
MH  - Humans
MH  - *Molecular Docking Simulation
MH  - Protein Binding
MH  - Proteins/chemistry/metabolism
MH  - *Workflow
EDAT- 2013/05/28 06:00
MHDA- 2014/01/18 06:00
CRDT- 2013/05/28 06:00
PHST- 2013/05/28 06:00 [entrez]
PHST- 2013/05/28 06:00 [pubmed]
PHST- 2014/01/18 06:00 [medline]
AID - 10.1021/ci400115b [doi]
PST - ppublish
SO  - J Chem Inf Model. 2013 Jun 24;53(6):1447-62. doi: 10.1021/ci400115b. Epub 2013 
      Jun 12.