Challenges and approaches in 3D ligand-based drug design

5 December 2023
8am PST | 11am EST | 4pm GMT | 5pm CET


Discovery projects are often faced with limited protein structure information, making structure-based drug design impossible. Ligand-based methods provide a valuable alternative to allow you to identify new leads and scaffold hop, understand the physical basis of your structure-activity relationships and guide lead optimisation. 

Join Drs Ajay Jain and Ann Cleves, Vice Presidents of Optibrium’s BioPharmics Division, experts in ligand and structure-based drug design, as they discuss the eSim molecular similarity method, a ligand-based drug design approach which considers surface-shape, electrostatics, and directionally sensitive hydrogen-bonding when comparing two molecules. 

Watch, as they share: 

  • The scientific foundations of the eSim approach 
  • The applications of this method, including virtual screening, pose prediction, and multiple ligand alignment
  • A hands-on demonstration of multiple ligand alignment using the StarDrop eSim3D module, and practical application within a virtual screen 

The webinar will be followed by a Q&A session, so feel free to come primed with any questions you have around ligand-based drug design. 

Register to attend the webinar

Meet the speakers

Dr Ajay Jain, Founder and CEO, BioPharmics

Dr Ajay Jain


Ajay has a PhD in Computer Science from Carnegie Mellon University following dual BS degrees in Biochemistry and in Computer Science from the University of Minnesota. Ajay has over 30 years of experience working in the field of computer-aided drug design. He held a series of senior scientific roles in multiple small biopharma companies, beginning with Arris Pharmaceutical in 1992 where he and his group pioneered new approaches to ligand- and structure-based drug design. He was also faculty at the University of California, San Francisco (UCSF) for over two decades, with a broad research program including both CADD and bioinformatics. Ajay founded BioPharmics LLC in 1998, which became the BioPharmics Division of Optibrium in August 2023.

Dr Ann Cleves Jain VP of Research, Optibrium

Dr Ann Cleves


Ann has a PhD in Microbiology and Cell Biology from the University of Illinois, followed by work in Biochemistry as a Helen Hay Whitney post-doctoral fellow at the University of California, San Francisco (UCSF). She moved to small biopharma beginning with MetaXen in 1997, leading many aspects of biological research and complex assay development across multiple projects. Ann’s research focus shifted to the causal linkages between molecular structure and human pharmacology. Her research spanned both the academic environment of UCSF and the applied realm within BioPharmics LLC since its founding in 1998. Ann has a deep understanding of how to solve challenging problems in pre-clinical pharmaceutical discovery using sophisticated computational approaches for ligand- and structure-based predictive modeling. BioPharmics LLC became the BioPharmics Division of Optibrium in August 2023.