Senior Software Engineer, Platform

Posted: Sep. 17, 2020

Company Overview

Silicon Therapeutics (“SITX”) is a privately held, physics-driven integrated drug discovery compa-ny in the preclinical IND stage targeting innate immunity to start, but with the capability to move into many other franchise opportunities. The Company’s initial pipeline is focused on modulation of the innate immune system to “light the spark” within immunologically cold tumors by using its physics-enabled drug discovery engine for the design of small molecule therapeutics and the lead program is in late stage preclinical studies. SITX’s discovery efforts as well as physics-based plat-form are all completely in-house, with a full wet lab as well as a team of over 25 experienced R&D professionals spanning biology, biochemistry, chemistry, biophysics (NMR + X-ray) & preclinical sciences. SITX’s engine leverages quantum mechanics and molecular dynamics, which are de-ployed on its own internal supercomputer composed of over 400 GPU’s and FPGA’s and allows SITX to accurately simulate the physical motion and properties of biological targets at an atomistic level resolution. The platform is completely proprietary to SITX and was built from the ground up with the purpose of addressing difficult targets and using simulations to break through bottlenecks that has plagued traditional drug discovery approaches on such targets. It is currently the ONLY company which owns the entire spectrum of physics-driven drug discovery from chip-to-clinic with a team of over 60 individuals in Boston.

The Company’s initial focus is on innate immunity and its pipeline is currently composed of one project entering IND-enabling studies, another one entering hit-to-lead and two more ramping up. It’s unique advantage in designing small molecules using all atom simulations has allowed it to advance a systemically available small molecule STING agonist into a preclinical development. The program is ramping up for IND enabling studies entry to the clinic in 2020. This differentiated product can be administered systemically via an IV dose and has single agent effects in early mouse efficacy studies using PD1 resistant tumor models and is a “rule-of-5” compliant small molecule. Beyond this one program, the Company is also advancing an ADAR inhibitor which can be considered an innate immune checkpoint as well as a multitude of targets that explore Innate Immunity’s role in cancer biology.

Job Summary

Silicon Therapeutics is seeking a highly motivated, collaborative, and talented Senior Software Engineer to work in a multi-disciplinary organization with a focus on overcoming challenging drug discovery bottlenecks using advanced molecular simulation methods to complement our integrated experimental capabilities. 



  • Work closely with Silicon Tx scientists to design, develop, and deploy computational methods and software for our drug discovery efforts
  • Conceptualize, implement, and maintain software engineering best practices
  • Ensure scalability, extensibility, and portability of platform code
  • Create, integrate, and maintain databases for storage and access of results
  • Investigate latest trends and scientific advancements in data analytics and high performance computing and propose adoption where appropriate
  • Coordinate joint software development efforts between our Boston and Suzhou offices and facilitate their communications and collaborations 

Required Qualifications

  • Fluent speaker in English and Chinese with strong communication skills
  • Outstanding development skills
  • Demonstrated track record of overcoming challenging problems
  • Experience leading projects with geographically distributed teams
  • Strong knowledge of Python
  • Familiarity with version control (such as Git) and test-and-release (such as Jenkins) frameworks.
  • Flexible work hours to accommodate colleagues in China

Additional Preferred Qualifications

  • Ability to mentor other software engineers and manage outsourced software development projects
  • Experience with parallel programming, especially data-parallel, using MPI, OpenMP, OpenACC or CUDA C/C++/Fortran
  • Experience working with containers
  • Ability to manage HPC clusters (CPU and GPU based)
  • Experience in using/deploying workflow frameworks such as Airflow, CWL, etc. 
  • Experience with scientific computing systems and schedulers
  • Passionate about developing software to advance drug discovery

Silicon Therapeutics provides equal employment opportunities to all employees and applicants for employment and prohibits discrimination and harassment of any type without regard to race, color, religion, age, sex, national origin, disability status, genetics, protected veteran status, sexual orientation, gender identity or expression, or any other characteristic protected by federal, state or local laws.