PASS

PASS Logo
The acronym PASS stands for Prediction of Activity Spectra for Substances. Upon entering a structural formula of a chemical substance, the program returns the potential biological activities of this compound.
PASS has been well accepted by the community, and is now actively used in the field of medicinal chemistry, by both academic organizations and pharma companies.
There are over 300 third-party publications with references to PASS. Some of the most recent papers that provide experimental evaluation of PASS predictions are listed
here.
https://www.youtube.com/watch?v=jV2eABoog1w
Application areas
  • Medicinal chemistry
  • Computational chemistry
  • Drug discovery / drug development
  • Drug repositioning
  • Chemical toxicity
  • Safety assessment
  • Pharmacogenomics, chemogenomics
  • SAR (qualitative structure-activity relationship)
  • Natural compound effects
  • Translational research / translational medicine

Activity prediction for a chemical substance by PASS

The slide show demonstrating the look-and-feel of PASS can be found here as well as on our Facebook site. A particularly useful tool to analyze and utilize PASS results further is PharmaExpert.

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What PASS can do

The input compound can be submitted in MOLfile or SDfile format. The output contains the following predicted activities:
General overview of all biological activities assigned to the input compound (out of a list of 7527 items)
Pharmacotherapeutic effects (464; example: antimetastatic effect)
Biochemical mechanisms (3850; example: xanthine oxidase inhibitor)
Toxicity, i.e. adverse and toxic effects (321; example: arrhythmogenic)
Metabolism (195; example: CYP2D6 substrate)
Gene regulation expression (1610; example: VEGF expression inhibition)
Transporter-related activities (68; example: sodium/calcium exchanger inhibitor)

Free demo

Thank you very much for your interest in the programs PASS and PharmaExpert!

Please contact us and you will be provided with your free trial version.

 

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PASS packages

  • PASS
  • Standard software package, which includes the standard SAR base (Structure-Activity Relationship base). Current standard version of PASS can predict over 7.000 different biological activities.
  • PASS Pro
  • PASS Professional package provides all functions of PASS and the additional option to create, train and validate your proprietary SAR base. With this package, you could make your own and unique SAR base, and use it further for predictions on other compounds. Your own SAR base can be used as it is, or can be combined with the standard SAR base. Thus, locally you would have a unique variant of PASS.
  • PASS Light
  • With PASS Light, you can create, train and validate your proprietary SAR base, and use it for further predictions. The standard SAR base is not included.
  • PASS customized
  • According to your potential focus on particular types of biological activities, a customized variant of PASS can be made to predict a restricted number of activities as per your selection.
  • PASS product + PharmaExpert
  • Any of the products PASS, PASS Pro, PASS Light and PASS customized, can be ordered in a package with PharmaExpert.

Current statistics

  • Structure-activity relationship (SAR) Base contains 313,345 substances and 75,875 descriptors.
  • Number of predictable activity types is over 7,100

 

The basis > How it works

To execute the prediction, PASS requires a knowledge base about structure-activity relationships for compounds with known biological activities. This is provided by SAR Base, containing the analysis results obtained with an in-house training set of more than 250,000 compounds with known biological activities. This training set is continuously curated and expanded. SAR Base can also be replaced by an exclusive knowledge base, which can be created using in-house data. The knowledge base together with the user-defined constraints of biological activities of interest and relevant parameters provides PASS the starting point for the computational prediction.

PASS applications

  • Medicinal chemistry
  • Computational chemistry
  • Drug discovery / drug development
  • Drug repositioning
  • Chemical toxicity
  • Safety assessment
  • Pharmacogenomics, chemogenomics
  • SAR (qualitative structure-activity relationship)
  • Natural compound effects
  • Translational research / translational medicine

Information downloads

  • PASS Flyer (download; pdf, 0.4 MB)
  • PASS Presentation (download; pdf, 0.7 MB)
  • PASS Info (download; pdf, 0.87 MB)
  • List of with PASS applications

Publications

Subbarayan P.R. (2016). Impact and Challenges of Chemoinformatics in Drug Discovery. In: Artificial Neural Network for Drug Design, Delivery and Disposition, 2016, 141–152. Link.

Agarwal S., Baroliya P.K., Bhargava A., Tripathi I.P., Goswami A.K. (2016). Synthesis, characterization, theoretical prediction of activities and evaluation of biological activities of some sulfacetamide based hydroxytriazenes. Bioorg. Med. Chem. Lett., 26 (12), 2870-2873. Link.

Yakovlev D.S. (2016). Condensed azoles – novel class of serotonin receptors ligands. Dr. Sci. Thesis (Pharmacology, clinical pharmacology). Volgograd State Medical University, Volgograd, 2016. 339 p.p. (Rus). Full text.

Tinkov O.V. Quantitative assessment of relationships between the structure and toxicity, lipophilicity and solubility of ecologically hazardous compounds. Ph.D. Thesis (Organic chemistry). The T.G. Shevchenko Pridnestrovian State University, Tiraspol, 2016. 199 p.p. Full text.

Kabir M.S., Mahamoud M.S., Chakrabarty N., Ahmad S., Masum M.A., Hoque M.A., Hossain M.M., Rahman M.M., Uddin M.M. (2016). Antithrombotic and cytotoxic activities of four Bangladeshi plants and PASS prediction of their isolated compounds. J. Basic Clin. Physiol. Pharmacol., 27 (6), 659-666. PubMed.

Singh D., Goel R.K. (2016). Anticonvulsant mechanism of saponins fraction from adventitious roots of Ficus religiosa: possible modulation of GABAergic, calcium and sodium channel functions. Revista Brasileira de Farmacognosia, 26 (5), 579–585. Link.

Figurka O.M. Synthesis of new amino derivatives of 1,4-naphthoquinone and their biological activity. Ph.D. Thesis (Organic chemistry). Lviv Polytechnic National University, Lviv, Ukraine, 2016. 199 p.p. Full text.

Agung I.I.W., Kalim2, Siti Chandra W.B., Rahardjo B. (2016). Computational analysis for revealing the role of thymoquinone (active compound from ethanolic extract of Nigella sativa) as inhibitor of P65 NF-kb activation in preclampsia treatment. International Journal of Pharmaceutical and Clinical Research, 8 (5), 297-300. Full text.

Brazhkо O.O. The biological activity of the derivatives of 2-methyl-(phenyl) substituted (quinoline-4-ylthio) carboxylic acids. Ph.D. Thesis (Bioorganic chemistry). Institute of Bioorganic Chemistry and Petrochemistry NAS of Ukraine, Kiev, Ukraine, 2016. 242 p.p. Link.

Mathew B., Suresh J., Anbazhagan S., Chidambaranathan N. (2016). Discovery of some novel imines of 2-amino, 5-thio, 1,3,4-thiadiazole as mucomembranous protector. Synthesis, anti-oxidant activity and in silico PASS approach. Journal of Saudi Chemical Society, 20 (Supplement 1), S426–S432. Link.

Habibyar A.F., Sharma N., Khurana N. (2016). PASS assisted prediction and pharmacological evaluation of hesperidin against scopolamine induced amnesia in mice. Eur. J. Pharmacol., 789, 385-394. Link.

Patil K.S., Bhalsing S.R. (2016). Ethnomedicinal uses, phytochemistry and pharmacological properties of the genus Boerhavia. J. Ethnopharmacol., 182, 200-220. Link.

Mohd Fauzi F., John C.M., Karunanidhi A., Mussa H.Y., Ramasamy R., Adam A., Bender A. (2016). Understanding the mode-of-action of Cassia auriculata via in silico and in vivo studies towards validating it as a long term therapy for type II diabetes. J. Ethnopharmacol., Available online 22 July 2016. Link.

Abdou W.M., Ganoub N.A., Ismail M.A.H., Sabry E., Barghash R.F., Geronikaki A. (2016). Developing efficient protocols for synthesis, antiosteoarthritic, antiinflammatory assessments and docking studies of nitrogen-containing bisphosphonate derivatives. Arabian Journal of Chemistry, Available online 10 March 2016. Link.

Shana Parveen S., Al-Alshaikh M.A., Panicker C.Y., El-Emamd A.A., Arisoye M., Temiz-Arpacie O., Van Alsenoy C. (2016). Synthesis, vibrational spectroscopic investigations, molecular docking, antibacterial and antimicrobial studies of 5-ethylsulphonyl-2-(p-aminophenyl) benzoxazole. Journal of Molecular Structure, 1115, 94-104. Link.

Agrawal M., Deval V., Gupta A., Sangala B.R., Prabhu S.S. (2016). and biological activity spectra of 4-(6-methoxy-2-naphthyl)-2-butanone using spectroscopic techniques. Spectrochim. Acta A. Mol. Biomol. Spectrosc., 167, 142-156. PubMed.

Srivastava A.K., Kumar A., Misra N., Manjula P.S.,. Sarojini B.K, Narayana B. (2016). Synthesis, spectral (FT-IR, UV-visible, NMR) features, biological activity prediction and theoretical studies of 4-amino-3-(4-hydroxybenzyl)-1H-1,2,4-triazole-5(4H)-thione and its tautomer. Journal of Molecular Structure, 1107, 137-144. Link.

Subashini K., Periandy S. (2016). Spectroscopic (FT-IR, FT-Raman, UV, NMR, NBO) investigation and molecular docking study of (R)-2-amino-1-phenylethanol. Journal of Molecular Structure, 1118, 240–256. Link.

Xavier S., Periandy S., Carthigayan K., Sebastian S. (2016). Molecular docking, TG/DTA, molecular structure, harmonic vibrational frequencies, natural bond orbital and TD-DFT analysis of diphenyl carbonate by DFT approach. Journal of Molecular Structure, 1125, 204–216. Link.

Galkina M.A., Bodrin G.V., Goryunov E.I., Goryunova I.B., Sherstneva A.S., Urmambetova J.S., Kolotyrkina N.J., Il’in M.V., Brel V.K., Kochetkov K.A. (2016). Mendeleev Communications, 25 (1), 75–76. Link.

Gillbro J.M., Lundahl M., Westman M., Baral R., Al-Bader T., Mavon A. (2015). Structural activity relationship analysis (SAR) and in vitro testing reveal the anti-ageing potential activity of acetyl aspartic acid. Int. J. Cosmet. Sci., 37 (Suppl 1), 15-20. Full text.

Patel H., Sonawane Y., Jagtap R., Dhangar K., Thapliyal N., Surana S., Noolvi M., Shaikh M.S., Rane R.A., Karpoormath R. (2015). Structural insight of glitazone for hepatotoxicity: Resolving mystery by PASS. Bioorg. Med. Chem. Lett., 25 (9), 1938-1946. Link.

Gawande D.Y., Goel .RK. (2015). Pharmacological validation of in-silico guided novel nootropic potential of Achyranthes aspera L. J. Ethnopharmacol., 175, 324-334. Link.

Siraj F.M., Natarajan S., Huq M.A., Kim Y.J., Yan D.C. (2015). Structural investigation of ginsenoside Rf with PPARg major transcriptional factor of adipogenesis and its impact on adipocyte. J. Ginseng Res, 39, 141-147. Full text.

Barenboim G.M., Borisov V.M., Golosov V.N., Saveca A.Yu. New problems and opportunities of oil spill monitoring systems. In: Hydrological Sciences and Water Security: Past, Present and Future. IAHS Press, 2015, p. 64-74. Link.

Jamuna S., Karthika K., Paulsamy S., Thenmozhi K., Kathiravan S., Venkatesh R. (2015). Confertin and scopoletin from leaf and root extracts of Hypochaeris radicata have anti-inflammatory and antioxidant activities. Industrial Crops and Products, 70, 221–230. Link.

Sudiwati N.L.P.E., Nurseta T., Aulanni’am A., Ali M. (2015). In-vitro and in-silico anticancer activity of parasitic tea plant Scurrula atropurpurea (Blume) Danser against cervical cancer. International Journal of PharmTech Research, 8 (7), 12-18. Full text.

Kaserer T., Temml V., Kutil Z., Vanek T., Landa P., Schuster D. (2015). Prospective performance evaluation of selected common virtual screening tools. Case study: Cyclooxygenase (COX) 1 and 2. Eur. J. Med. Chem., 96, 445-457. Link.

Nassar N.N., Al-Shorbagy M.Y., Arab H.H., Abdallah D.M. (2015). Saxagliptin: a novel antiparkinsonian approach. Neuropharmacology, 89, 308–317. Link.

Pospieszny T. (2015). Steroidal Conjugates: Synthesis, Spectroscopic, and Biological Studies. Studies in Natural Products Chemistry, 46, 169–200. Link.

Makarova E.A. Computational prediction and experimental rationales for searching neurotrophic agents among the compounds with four-coordinate phosphorus. Ph.D. Thesis (Pharmacology, clinical pharmacology). Kazan State Medical University, Kazan, Russia, 2015. 141 p.p. Full text.

Iqbal S.S., Gurumurthy P., Pravinkumar P., Pawankumar, Pillai K.S. (2015). GC-MS analysis, heavy metal content and predication of anti-diabetic activity spectra of a novel polyherbal formulation. International Journal of Applied Research, 1 (6), 276-281. Full text.

Fazal E., Panicker C.Y., Varghese H.T., Nagarajan S., Sudha B.S., War J.A., Srivastava S.K., Harikumar B., Anto P.L. (2015). Vibrational spectroscopic and molecular docking study of 4-Methylphenylquinoline-2-carboxylate. Spectrochim. Acta. A Mol. Biomol. Spectrosc., 143, 213-222. Link.

Golovnev N.N., Molokeev M.S., Sterkhova I.V., Goryunov Yu.V., Atuchin V.V. (2015). New class of bicyclic compounds derived from thiobarbituric acid with representative compound 1,3-diethyl-7-hydroxy-5,5,7-trimethyl-2-thioxo-1,2,3,5,6,7-hexahydro-4H-pyrano[2,3-d]pyrimidin-4-one. Preparation, crystal structure, mass spectrometry and IR spectroscopy. Journal of Molecular Structure, 1102, 101–107. Link.

Patel H., Dhangar K., Sonawane Y., Surana S., Karpoormath R., Thapliyal N., Shaikh M., Noolvi M., Jagtap R. (2015). In search of selective 11b-HSD type 1 inhibitors without nephrotoxicity: An approach to resolve the metabolic syndrome by virtual based screening. Arabian Journal of Chemistry, Available online 21 August 2015. Link.

Mary Y.S., Varghese H.T., Panicker C.Y., Girisha M., Sagar B.K., Yathirajan H.S., Al-Saadi A.A., Van Alsenoy C. (2015).Vibrational spectra, HOMO, LUMO, NBO, MEP analysis and molecular docking study of 2,2-diphenyl-4-(piperidin-1-yl)butanamide. Spectrochim. Acta. A Mol. Biomol. Spectrosc., 150, 543-556. Link.

Ariffin A., Rahman N.A., Yehye W.A., Alhadi A.A., Kadir F.A. (2014). PASS-assisted design, synthesis and antioxidant evaluation of new butylated hydroxytoluene derivatives. Eur. J. Med. Chem., 87, 564-577. Link.

Mathew B., Suresh J., Anbazhagan S., Dev S. (2014). Proposed interaction of some novel antidepressant pyrazolines against monoamine oxidase isoforms. Molecular docking studies and PASS assisted in silico approach. Biomedicine & Aging Pathology, 4 (4), 297–301. Link.

Jamkhandea P.G., Wattamwara A.S., Pekamwara S.S., Chandak P.G. (2014). Antioxidant, antimicrobial activity and in silico PASS prediction of Annona reticulata Linn. root extract. Beni-Suef University Journal of Basic and Applied Sciences, 3 (2), 140–148. Link.

Sharipov I.M. Synthesis and biological activity of thiethane-containing derivatives of 4,5-dibromidasole. Ph.D. Thesis (Pharmaceutical chemistry, pharmacognosy). Samara State Medical University, Samara, Russia, 2014. Link.

Iskakova T.K., Ibrayeva S.S., Praliyev K.S., Malmakova A.Ye., Baktybaeva L.K., Seilkhanov T.M. (2014). Synthesis and myelostimulatory activity of 1-(2-ethoxyethyl) piperidine derivatives. Procedia Chemistry, 10, 358–363. Link.

Hernández-Vázquez E., Aguayo-Ortiz R., Ramírez-Espinosa J.J., Estrada-Soto S., Hernández-Luis F. (2013). Synthesis, hypoglycemic activity and molecular modeling studies of pyrazole-3-carbohydrazides designed by a CoMFA model. Eur. J. Med. Chem., 69, 10-21. Link.

Singh S.P., Gogoi D., Bezbaruah R.L., Bordoloi M.J., Barua N.C. (2013). Virtual screening on potential neuraminidase inhibitors of influenza A virus H1N1. Drug Invention Today, 5 (3) 241–245. Link.

Pospieszny T., Koenig H., Brycki B. (2013). Synthesis and spectroscopic studies of new quasi podands from bile acid derivatives. Tetrahedron Letters, 54 (35), 4700–4704. Link.

Khristova T. Computer-aided design on novel antithrombotic agents. Ph.D. Thesis (Chemistry, Chemoinformatics). Strasbourg University, Strasbourg, 2013. 193 p.p. Full text.

B-Rao C., Kulkarni-Almeida A., Katkar K.V., Khanna S., Ghosh U., Keche A., Shah P., Srivastava A., Korde V., Nemmani K.V., Deshmukh N.J., Dixit A., Brahma M.K., Bahirat U., Doshi L., Sharma R., Sivaramakrishnan H. (2012). Identification of novel isocytosine derivatives as xanthine oxidase inhibitors from a set of virtual screening hits. Bioorg. Med. Chem., 20 (9), 2930-2939. Link.

Kumar A., Lohan P., Aneja D.K., Gupta G.K., Kaushik D., Prakash O. (2012). Design, synthesis, computational and biological evaluation of some new hydrazino derivatives of DHA and pyranopyrazoles. Eur. J. Med. Chem., 50, 81-89. Link.

Dhanachandra S.Kh., Karthikeyan M., Kirubakaran P., Nagamani S. (2011). Pharmacophore filtering and 3D-QSAR in the discovery of new JAK2 inhibitors. J. Mol. Graph. Model., 30, 186-197. Link.

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