Publications
Presentations
- Reverse Screen: Given One Molecule, Which Proteins Does It Bind? 40 Hours of Docking to 108 Seconds Reverse screening and the retrieval step in front of docking, with reversescreen.ai.
- Two Comparisons May Be All We Need: A Foundation Model for Drug Discovery That Ranks, Not Predicts How the Family Foundation Model ranks compounds and targets, with familyfoundationmodel.com.
- Building a business with and without scientific computing: The five W's and one H (San Diego ACS, 2016) PDF KEY PPT M4V
- New strategies to engage more of the world with scientific app development and content deployment (San Francisco ACS, 2014) PDF PPT
- Standing on the Shoulders of Giants: New strategies to involve more of the world with data mining and intelligence extraction (Nice, France - International 2014 II-SDV conference, 2014) PDF PPT
- Expanding the Reach of ChemInformatics through Mobile Computing (New Orleans ACS, 2013) PDF
- Integrating proprietary and public-domain data from Kinase publications and patents from a biopharmaceutical company's perspective. (Webinar, Sept 25, 2012) PDF
- Why Future Medicines Will Need to be Discovered in the Cloud (San Francisco Bio-IT World Cloud Summit, 2012) PDF
- Having a mobile app presence - necessary or nice to have (San Diego ACS, 2012) PDF
- Using Structural and Receptor-Site Similarity to Generate New Matter Ideas (Denver ACS, 2011) PDF
- Riding the Mobile Wave (Denver ACS, 2011) PDF
- Catching the Mobile Wave WEB
- The Mobile Kinome (ChemAxon UGM, Budapest-5/20/10) - PDF
- Using knowledgebases of structure-activity-data, receptor-site and protein structural similarity to generate new matter ideas (ACS-D.C.-8/16/09) - PDF
- Using Sequence-, Structure- and Receptor-site Similarity to Generate New Matter Ideas within the Kinome (Accelrys Life Science Forums-6/09) - PDF
- Using Receptor-Site and Protein Structure Similarity to Generate New Matter Ideas (UK QSAR-5/14/09) - PDF
- Using Receptor-Site Similarity to LigandCross into New Diversity (CHI Fragment-Based Techniques-4/8/09) - PDF
- Exercising receptor-site similarity: From Off-Target Identification to Scaffold Hopping (ACS-8/17/08) - PDF
- Surveying ligand- and target-based similarities within the Kinome (ACS-8/17/08) - PDF
- Interrogating the Druggable Proteome: Target-Fishing and Drug Design (Beijing-10/23/08) - PDF
- Eidogen-Sertanty Technology Overview (09/1/06) - PDF
- Eidogen-Sertanty Product Summary - PDF
Papers
- ReverseScreen.ai: Pharmacophore-Guided Reverse Screening Across the Growing Co-Complex Proteome Muskal, S. M. (ORCID); Nicola, G. bioRxiv, first posted 15 September 2026, version 1 (DOI: 10.64898/2026.09.09.750461). CC BY 4.0. The method behind reversescreen.ai.
- PharmCast: rapid generation of three-dimensional pharmacophore fingerprints from two-dimensional structure without conformer generation Muskal, S. M. (ORCID); McGregor, M. J. bioRxiv, first posted 7 September 2026, version 2 (DOI: 10.64898/2026.09.02.748999). CC BY 4.0. Describes PharmCast version 10.
- High quality, small molecule-activity datasets for kinase research F1000Research. June 14, 2016 (DOI: 10.12688/f1000research.8950.2)
- Lovastatin lactone may improve irritable bowel syndrome with constipation (IBS-C) by inhibiting enzymes in the archaeal methanogenesis pathway F1000Research. April 8, 2016 (DOI: 10.12688/f1000research.8406.3) Figure 4. Lovastatin-lactone v. F420 in the A5UMI1 site
- Kinome-wide Activity Modeling from Diverse Public High-Quality Data Sets J. Chem. Inf. Model. August 24, 2012 (DOI: 10.1021/ci300403k)
- Novel Kinase Inhibitors by Reshuffling Ligand Functionalities Across the Human Kinome J. Chem. Inf. Model. November 5, 2012 (DOI: 10.1021/ci3003842)
- Reaction101 and Yield101: Two mobile apps for chemistry with pedagogical value Whitepaper (2011)
- Interrogating the druggable genome with structural informatics MolecularDiversity (2006)
- StructSorter: A Method for Continuously Updating a Comprehensive Protein Structure Alignment Database J. Chem. Inf. Model. 2006, 46, 1871-1876
- STRUCTFAST: Protein Sequence Remote Homology Detection and Alignment Using Novel Dynamic Programming and Profile-Profile Scoring Proteins. 2006 64:960-967
- Convergent Island Statistics: A fast method for determining local alignment score significance. Bioinformatics, 2005, 21, 2827-2831.
- Prospective Exploration of Synthetically Feasible, Medicinally Relevant Chemical Space J.Chem. Inf. Model. 2005, 45, 239-248
- Pharmacophore Fingerprinting. 1. Application to QSAR and Focused Library Design
J. Chem. Inf. Comput. Sci. 1999, 39, 569-574
- Pharmacophore Fingerprinting. 2. Application to Primary Library Design
J Chem Inf. Comput. Sci. 2000, 40, 117-25
- A Simple and Readily Integratable Approach to Toxicity Prediction J. Chem. Inf. Comput. Sci. 2003, 43, 1673-1678
- Prediction of Human Intestinal Absorption of Drug Compounds from Molecular Structure J. Chem. Inf. Comput. Sci. 1998, 38, 726-735
Demos
