Principal Computational Scientist, Protein Engineering
Encodia, Inc., United States

Encodia is a rapidly growing platform company that is developing a new generation of protein analysis tools based on single-molecule protein sequencing. Our goal is to make protein sequencing easy and ubiquitous by using a novel reverse-translation technology that turns peptide sequences into DNA. The DNA can be read by a DNA sequencer, providing a path to breakthrough proteomics research at a scale that is not practical or cost-effective using current technologies.

We are seeking an experienced, motivated, and innovative Computational Scientist to join our Protein Engineering team. The ideal candidate should be an excellent collaborator and have experience applying state-of-the-art machine learning and computational methods to design novel peptides and proteins, such as structural modeling and prediction, structure library

generation, molecular docking, and multiparameter molecular property optimization.

• Develop and implement a computational platform for designing proteins, de novo proteins using state-of-the-art computational
• modeling, simulation, docking and machine learning approaches.
• Design proteins with new functional properties using rational protein engineering methods, and apply these in-silico predictions to lead the development process.
• Discover new scaffolds/structure-function relationships and macromolecular design principles based on experimental data and
• metagenomic datasets.
• Work closely with molecular biology, biochemistry, protein science, and bioinformatics teams to improve an iterative scientific workflow.
• Train and direct junior scientists for protein design and characterization to improve desired properties
• Prepare and review patent documentation
• Analyze, interpret, document and present data to the scientific and leadership team
• Write internal scientific reports and articles for publication
• Maintain a broad awareness of the developments in computational protein design
• Work within a collaborative, and interdisciplinary team to actively contribute to creating, shaping, and executing the vision of the company

Requirements

• PhD or equivalent in computational biology, computational chemistry, biochemistry, molecular Biology, structural biology, or related field of study
• 10+ years experience in computational protein design, modeling, simulation, structure-function prediction, and NGS
• Proficient in Python and significant experience with relevant macromolecular modeling software (i.e. PyRosetta, AlphaFold, MOE, Schrödinger, Discovery studio)
• Fluent coding skills in one or more programming languages (e.g. Python, C++, or MATLAB, R, bash, Linux and unix commands.
• Experience working with molecular biology and synthetic biology teams for making DNA libraries (combinatorial libraries, site saturation libraries)
• Experience with cloud computing (i.e. AWS) and software
• Experience with computational and bioinformatic methods related to gene and protein discovery and characterization
• Proven ability to work across teams of software engineers, data scientists, proteomics, and chemistry to develop protein sequencing platforms.
• Familiar with directed evolution including yeast/phage/snap display, bioinformatics, NGS data analysis for library enrichment

• Work independently for designing protein with desired attributes using in-silico methods as well as biochemical techniques.
• Have a track record of designing experiments, coordinating with team members, and collaborating across disciplines to accomplish projects with deadlines.
• Develop computational and experimental methods to develop workflow for library construction, high throughput screening, and hit validation
• Work with protein science for protein production, biochemical characterization and deliver proteins for developing a disruptive
• technology
• Work with molecular biology teams for primer design, cloning, and mutagenesis
• Engage with members of the team in troubleshooting, data analysis, and data interpretation.
• Be self-motivated and able to contribute effectively in a fast-changing environment
• Have high integrity and ethics
• Be committed to quality and timely delivery of results
• Maintain accurate and well-organized laboratory notebooks
• Respect laboratory safety policies and practices

Benefits

Encodia is an Equal Opportunity Employer. We offer a competitive and comprehensive employee benefits package including medical plans, dental insurance, vision plans, LTD, paid vacation, and a stock plan.

We do not discriminate in recruitment, hiring, training, promotion or other

Job Rewards and Benefits