Welcome to the PyRx Website
PyRx is a Virtual Screening software for Computational Drug Discovery that can be used to screen libraries of compounds against potential drug targets. PyRx enables Medicinal Chemists to run Virtual Screening from any platform and helps users in every step of this process - from data preparation to job submission and analysis of the results. While it is true that there is no magic button in the drug discovery process, PyRx includes docking wizard with an easy-to-use user interface which makes it a valuable tool for Computer-Aided Drug Design. PyRx also includes chemical spreadsheet-like functionality and powerful visualization engine that are essential for structure-based drug design. Please visit
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0.8 and earlier versions
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PyRx is using large body of established open source software including:
The following are publications where PyRx has been mentioned. Please let us know if we miss any citation. Thank you all for using PyRx!
Virtual Screening for Potential Inhibitors of NS3 Protein of Zika Virus. Sahoo M, Jena L, Daf S, Kumar S. Genomics Inform. 2016 Sep;14(3):104-111.
Flurbiprofen-antioxidant mutual prodrugs as safer nonsteroidal anti-inflammatory drugs: synthesis, pharmacological investigation, and computational molecular modeling. Ashraf Z, Alamgeer, Kanwal M, Hassan M, Abdullah S, Waheed M, Ahsan H, Kim SJ. Drug Des Devel Ther. 2016 Jul 27;10:2401-19.
The Response Regulator BfmR Is a Potential Drug Target for Acinetobacter baumannii. Russo TA, Manohar A, Beanan JM, Olson R, MacDonald U, Graham J, Umland TC. mSphere. 2016 May 11;1(3). pii: e00082-16.
A Novel Phenanthridionone Based Scaffold As a Potential Inhibitor of the BRD2 Bromodomain: Crystal Structure of the Complex. Tripathi S, Mathur S, Deshmukh P, Manjula R, Padmanabhan B. PLoS One. 2016 May 31;11(5):e0156344.
Novel Anthra[1,2-c][1,2,5]Thiadiazole-6,11-Diones as Promising Anticancer Lead Compounds: Biological Evaluation, Characterization & Molecular Targets Determination. Ali AA, Lee YR, Chen TC, Chen CL, Lee CC, Shiau CY, Chiang CH, Huang HS. PLoS One. 2016 Apr 21;11(4):e0154278.
Allosteric inhibitors of Coxsackie virus A24 RNA polymerase. Schein CH, Rowold D, Choi KH. Bioorg Med Chem. 2016 Feb 15;24(4):570-7.
Mining ZINC Database to Discover Potential Phosphodiesterase 9 Inhibitors Using Structure-Based Drug Design Approach. Hassaan EA, Sigler SC, Ibrahim TM, Lee KJ, Cichon LK, Gary BD, Canzoneri JC, Piazza GA, Abadi AH. Med Chem. 2016;12(5):472-7.
Molecular docking based virtual screening of compounds for inhibiting sortase A in L.monocytogenes.Rashidieh B, Madani Z, Azam MK, Maklavani SK, Akbari NR, Tavakoli S, Rigi G. Bioinformation. 2015 Nov 30;11(11):501-5.
JAK3 inhibitor VI is a mutant specific inhibitor for epidermal growth factor receptor with the gatekeeper mutation T790M. Nishiya N, Sakamoto Y, Oku Y, Nonaka T, Uehara Y. World J Biol Chem. 2015 Nov 26;6(4):409-18.
Molecular structure-function relationship of dietary polyphenols for inhibiting VEGF-induced VEGFR-2 activity. Cerezo AB, Winterbone MS, Moyle CW, Needs PW, Kroon PA. Mol Nutr Food Res. 2015 Nov;59(11):2119-31.
279Val→Phe Polymorphism of lipoprotein-associated phospholipase A2 resulted in changes of folding kinetics and recognition to substrate. Masbuchin AN, Rohman MS, Putri JF, Cahyaningtyas M, Widodo. Comput Biol Chem. 2015 Oct 19;59(Pt A):199-207.
A molecular modeling based screening for potential inhibitors to alpha hemolysin from Staphylococcus aureus. Rashidieh B, Etemadiafshar S, Memari G, Mirzaeichegeni M, Yazdi S, Farsimadan F, Alizadeh S. Bioinformation. 2015 Aug 31;11(8):373-7.
In silico analysis and molecular docking studies of potential angiotensin-converting enzyme inhibitor using quercetin glycosides. Muhammad SA, Fatima N. Pharmacogn Mag. 2015;11:S123-6.
Structural Studies of the HIV-1 Integrase Protein: Compound Screening and Characterization of a DNA-Binding Inhibitor. Quashie PK, Han YS, Hassounah S, Mesplède T, Wainberg MA. PLoS One. 2015 Jun 5;10(6):e0128310.
Identification of ALK5 inhibitor via structure-based virtual screening and ADMET prediction. Lin A, Cai Z, Hu G, Li Q. J Recept Signal Transduct Res. 2015 Jun 4:1-6.
Molecular docking based screening of predicted potential inhibitors for VP40 from Ebola virus. Abazari D, Moghtadaei M, Behvarmanesh A, Ghannadi B, Aghaei M, Behruznia M, Rigi G. Bioinformation. 2015 May 28;11(5):243-7.
Virtual screening for potential inhibitors of high-risk human papillomavirus 16 E6 protein. Kumar S, Jena L, Mohod K, Daf S, Varma AK. Interdiscip Sci. 2015 Feb 6.
Small-Molecule Library Screening by Docking with PyRx. Dallakyan S, Olson AJ. Methods Mol Biol. 2015;1263:243-50.
Identification of Anti-Cancer Targets of Eco-Friendly Waste Punica granatum Peel by Dual Reverse Virtual Screening and Binding Analysis. Usha T, Goyal AK, Lubna S, Prashanth H, Mohan TM, Pande V, Middha SK. Asian Pac J Cancer Prev. 2014;15(23):10345-50.
A potential target of Tanshinone IIA for acute promyelocytic leukemia revealed by inverse docking and drug repurposing. Chen SJ. Asian Pac J Cancer Prev. 2014;15(10):4301-5.
Identification of a potential anticancer target of danshensu by inverse docking. Chen SJ, Ren JL. Asian Pac J Cancer Prev. 2014;15(1):111-6.
Histone deacetylase inhibitors equipped with estrogen receptor modulation activity. Gryder BE, Rood MK, Johnson KA, Patil V, Raftery ED, Yao LP, Rice M, Azizi B, Doyle DF, Oyelere AK. J Med Chem. 2013;56(14):5782-96.
Selectively targeting prostate cancer with antiandrogen equipped histone deacetylase inhibitors. Gryder BE, Akbashev MJ, Rood MK, Raftery ED, Meyers WM, Dillard P, Khan S, Oyelere AK. ACS Chem Biol. 2013;8(11):2550-60.
A chemogenomics based approach for deorphanization of testicular receptor 4: An orphan receptor of nuclear receptor superfamily. Deshmukh S, Madagi SB. J Nat Sci Biol Med. 2013; 4(2):276-281.
Identification of proapoptopic, anti-inflammatory, anti- proliferative, anti-invasive and anti-angiogenic targets of essential oils in cardamom by dual reverse virtual screening and binding pose analysis. Bhattacharjee B, Chatterjee J. Asian Pac J Cancer Prev. 2013;14(6):3735-42.
Identifications small molecules inhibitor of p53-mortalin complex for cancer drug using virtual screening. Utomo DH, Widodo N, Rifa'i M. 2012;8(9):426-9. Bioinformation.
Accessible high-throughput virtual screening molecular docking software for students and educators. Jacob RB, Andersen T, McDougal OM. 2012 May;8(5):e1002499. PLoS Comput Biol.
Virtual screening of Indonesian herbal database as HIV-1 reverse transcriptase inhibitor. Syahdi RR, Mun'im A, Suhartanto H, Yanuar A. Bioinformation. 2012;8(24):1206-10.
Molecular Docking of Aromatase Inhibitors. Suvannang N, Nantasenamat Ch, Isarankura-Na-Ayudhya Ch, Prachayasittikul V. Molecules 2011, 16(5), 3597-3617.