title: Ultrafast protein structure-based virtual screening with Panther.
abstract: Molecular docking is by far the most common method used in protein structure-based virtual screening. This paper presents Panther, a novel ultrafast multipurpose docking tool. In Panther, a simple shape-electrostatic model of the ligand-binding area of the protein is created by utilizing the protein crystal structure. The features of the possible ligands are then compared to the model by using a similarity search algorithm. On average, one ligand can be processed in a few minutes by using classical docking methods, whereas using Panther processing takes <1 s. The presented Panther protocol can be used in several applications, such as speeding up the early phases of drug discovery projects, reducing the number of failures in the clinical phase of the drug development process, and estimating the environmental toxicity of chemicals. Panther-code is available in our web pages (http://www.jyu.fi/panther) free of charge after registration.
authors.affiliation: Department of Biological and Environmental Science & Nanoscience Center, University of Jyvaskyla, P.O. Box 35, 40014, University of Jyvaskyla, Finland.
authors.forename: Sanna P
authors.initials: SP
authors.lastname: Niinivehmas
authors.affiliation: Department of Biological and Environmental Science & Nanoscience Center, University of Jyvaskyla, P.O. Box 35, 40014, University of Jyvaskyla, Finland.|Faculty of Health Sciences, School of Pharmacy, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland.
authors.forename: Kari
authors.initials: K
authors.lastname: Salokas
authors.affiliation: Department of Biological and Environmental Science & Nanoscience Center, University of Jyvaskyla, P.O. Box 35, 40014, University of Jyvaskyla, Finland.|Faculty of Health Sciences, School of Pharmacy, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland.
authors.forename: Sakari
authors.initials: S
authors.lastname: Lätti
authors.affiliation: Faculty of Health Sciences, School of Pharmacy, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland.
authors.forename: Hannu
authors.initials: H
authors.lastname: Raunio
authors.affiliation: Department of Biological and Environmental Science & Nanoscience Center, University of Jyvaskyla, P.O. Box 35, 40014, University of Jyvaskyla, Finland. olli.t.pentikainen@jyu.fi.
authors.forename: Olli T
authors.initials: OT
authors.lastname: Pentikäinen
mesh_terms: D000465:Algorithms; D019540:Area Under Curve; D001665:Binding Sites; D062126:Databases, Chemical; D004353:Drug Evaluation, Preclinical / Q000379:methods*; D047628:Estrogen Receptor alpha / Q000737:chemistry / Q000378:metabolism; D008024:Ligands; D062105:Molecular Docking Simulation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012372:ROC Curve; D012984:Software; D055672:Static Electricity; D013329:Structure-Activity Relationship
chemical_list: C506487:ESR1 protein, human; D047628:Estrogen Receptor alpha; D008024:Ligands; D011506:Proteins
keywords: Molecular docking; Panther; Similarity search; Virtual screening