Postdoctoral Fellow - Artificial Intelligence and Machine Learning Strategies for Antibody-Antigen and Protein-Protein Affinity Prediction (Hybrid)

Job Description

Be a part of the legacy: Postdoctoral Research Fellow Program

Our Research Laboratories’ Postdoctoral Research Fellow Program aims to be a best-in-industry program for industrial postdoctoral researchers, designed to provide you with an academic focus in a commercial environment. With the resources, reach, and expertise of a large pharmaceutical company, postdoctoral researchers will be positioned to excel in an institution committed to breakthrough innovation in research and discovery.
 

Position Overview:

We are seeking a talented and motivated Postdoctoral Scientist with expertise in structural biology, computational chemistry, molecular dynamics, protein design or related field and a passionate motivation to learn and pursue AI/ML approaches to protein-protein interactions, with a focus on antibody antigen interactions. The postdoctoral researcher will work closely with our Research & Development Division data science and IT colleagues as well as interact with our Research & Development Division Protein Engineering center of excellence to curate data from the internal of our company's database and mine both internal resources and software to generate predictive models of antibody affinity or protein binding affinity.

Responsibilities include but are not limited to:

• Collection and data engineering of antibody-antigen or protein-protein interactions in our company's database with crystal structure data or modellable structure data.

• Collection and data engineering of display-based affinity data through next generation sequencing (NGS) collection.

• Evaluation of predictive accuracy on series-based data. Use cases include family data with a series of point mutations versus generalizable predictions based on structural and physics-based methods.

• Combination of large language models with structurally aware models, fine tuning and evaluation on predictive accuracy.

• Evaluation of deep learning models for prediction of antibody-antigen and protein-protein interactions.

• Publication of results.

• Maintenance of code repositories and documentation (our Research & Development Division Github environment)

• Complete required trainings.

• Attend and actively participate in department and group meetings.

• Attend and actively participate to our company's and external scientific symposiums and meetings/seminars.

• Literature mining.

• Write and review publications and manuscripts.

Education Minimum Requirement:  

• PhD in biology, biochemistry, structural biology (crystallography/cryo) or related field or completing PhD by May 2025.

Required Experience and Skills: 

• Strong expertise in an in silico computational discipline (e.g. structural biology, molecular dynamics, protein design)

• Strong familiarity with Linux/Unix operating systems and BASH usage/scripting

• Familiarity with Python programming/scripting, Jupyter notebooks or VSCode

• Familiarity with deep learning software (e.g. Pytorch, Huggingface)

• Familiarity with data science tools (e.g. Scikitlearn, Pandas, Matplotlib etc)

• Passionate motivation to stay up-to-date with cutting edge techniques in AI/ML guided protein design and prediction

• High attention to detail and scientific and technical problem solving

• Must have strong organizational skills to deal with large amounts of data

• The candidate should exhibit excellent communication and collaborative skills for working on cross-functional multi-disciplinary teams

Preferred Experience and Skills:

• Proficiency with BASH/HPC terminal environments and Python coding

• Proficiency/familiarity with deep learning software (e.g. Pytorch, Huggingface, Alphafold, Rosettafold, ESM)

• Previous experience with physics-based software (e.g. Rosetta, MOE, Schrodinger, Amber, GROMACS)

• Data science and engineering proficiency.

PostdoctoralOpportunities

Under New York City, Colorado State, Washington State, and California State law, the Company is required to provide a reasonable estimate of the salary range for this job. Final determinations with respect to salary will take into account a number of factors, which may include, but not be limited to the primary work location and the chosen candidate’s relevant skills, experience, and education.

Expected salary range:

$75,000.00-$86,000.00

Available benefits include bonus eligibility, health care and other insurance benefits (for employee and family), retirement benefits, paid holidays, vacation, and sick days. For Washington State Jobs, a summary of benefits is listed here. 

Current Employees apply HERE

Current Contingent Workers apply HERE

Secondary Language(s) Job Description

Be a part of the legacy: Postdoctoral Research Fellow Program

Our Research Laboratories’ Postdoctoral Research Fellow Program aims to be a best-in-industry program for industrial postdoctoral researchers, designed to provide you with an academic focus in a commercial environment. With the resources, reach, and expertise of a large pharmaceutical company, postdoctoral researchers will be positioned to excel in an institution committed to breakthrough innovation in research and discovery.
 

Position Overview:

We are seeking a talented and motivated Postdoctoral Scientist with expertise in structural biology, computational chemistry, molecular dynamics, protein design or related field and a passionate motivation to learn and pursue AI/ML approaches to protein-protein interactions, with a focus on antibody antigen interactions. The postdoctoral researcher will work closely with our Research & Development Division data science and IT colleagues as well as interact with our Research & Development Division Protein Engineering center of excellence to curate data from the internal of our company's database and mine both internal resources and software to generate predictive models of antibody affinity or protein binding affinity.

Responsibilities include but are not limited to:

• Collection and data engineering of antibody-antigen or protein-protein interactions in our company's database with crystal structure data or modellable structure data.

• Collection and data engineering of display-based affinity data through next generation sequencing (NGS) collection.

• Evaluation of predictive accuracy on series-based data. Use cases include family data with a series of point mutations versus generalizable predictions based on structural and physics-based methods.

• Combination of large language models with structurally aware models, fine tuning and evaluation on predictive accuracy.

• Evaluation of deep learning models for prediction of antibody-antigen and protein-protein interactions.

• Publication of results.

• Maintenance of code repositories and documentation (our Research & Development Division Github environment)

• Complete required trainings.

• Attend and actively participate in department and group meetings.

• Attend and actively participate to our company's and external scientific symposiums and meetings/seminars.

• Literature mining.

• Write and review publications and manuscripts.

Education Minimum Requirement:  

• PhD in biology, biochemistry, structural biology (crystallography/cryo) or related field or completing PhD by May 2025.

Required Experience and Skills: 

• Strong expertise in an in silico computational discipline (e.g. structural biology, molecular dynamics, protein design)

• Strong familiarity with Linux/Unix operating systems and BASH usage/scripting

• Familiarity with Python programming/scripting, Jupyter notebooks or VSCode

• Familiarity with deep learning software (e.g. Pytorch, Huggingface)

• Familiarity with data science tools (e.g. Scikitlearn, Pandas, Matplotlib etc)

• Passionate motivation to stay up-to-date with cutting edge techniques in AI/ML guided protein design and prediction

• High attention to detail and scientific and technical problem solving

• Must have strong organizational skills to deal with large amounts of data

• The candidate should exhibit excellent communication and collaborative skills for working on cross-functional multi-disciplinary teams

Preferred Experience and Skills:

• Proficiency with BASH/HPC terminal environments and Python coding

• Proficiency/familiarity with deep learning software (e.g. Pytorch, Huggingface, Alphafold, Rosettafold, ESM)

• Previous experience with physics-based software (e.g. Rosetta, MOE, Schrodinger, Amber, GROMACS)

• Data science and engineering proficiency.

PostdoctoralOpportunities

Under New York City, Colorado State, Washington State, and California State law, the Company is required to provide a reasonable estimate of the salary range for this job. Final determinations with respect to salary will take into account a number of factors, which may include, but not be limited to the primary work location and the chosen candidate’s relevant skills, experience, and education.

Expected salary range:

$75,000.00-$86,000.00

Available benefits include bonus eligibility, health care and other insurance benefits (for employee and family), retirement benefits, paid holidays, vacation, and sick days. For Washington State Jobs, a summary of benefits is listed here. 

US and Puerto Rico Residents Only:

Our company is committed to inclusion, ensuring that candidates can engage in a hiring process that exhibits their true capabilities. Please click here  if you need an accommodation during the application or hiring process.

We are an Equal Opportunity Employer, committed to fostering an inclusive and diverse workplace.  All qualified applicants will receive consideration for employment without regard to race, color, age, religion, sex, sexual orientation, gender identity, national origin, protected veteran status, or disability status, or other applicable legally protected characteristics.  For more information about personal rights under the U.S. Equal Opportunity Employment laws, visit:

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We are proud to be a company that embraces the value of bringing diverse, talented, and committed people together. The fastest way to breakthrough innovation is when diverse ideas come together in an inclusive environment. We encourage our colleagues to respectfully challenge one another’s thinking and approach problems collectively.

Learn more about your rights, including under California, Colorado and other US State Acts

U.S. Hybrid Work Model

Effective September 5, 2023, employees in office-based positions in the U.S. will be working a Hybrid work consisting of three total days on-site per week, Monday - Thursday, although the specific days may vary by site or organization, with Friday designated as a remote-working day, unless business critical tasks require an on-site presence.This Hybrid work model does not apply to, and daily in-person attendance is required for, field-based positions; facility-based, manufacturing-based, or research-based positions where the work to be performed is located at a Company site; positions covered by a collective-bargaining agreement (unless the agreement provides for hybrid work); or any other position for which the Company has determined the job requirements cannot be reasonably met working remotely. Please note, this Hybrid work model guidance also does not apply to roles that have been designated as “remote”.

San Francisco Residents Only: We will consider qualified applicants with arrest and conviction records for employment in compliance with the San Francisco Fair Chance Ordinance

Los Angeles Residents Only: We will consider for employment all qualified applicants, including those with criminal histories, in a manner consistent with the requirements of applicable state and local laws, including the City of Los Angeles’ Fair Chance Initiative for Hiring Ordinance

Search Firm Representatives Please Read Carefully 
Merck & Co., Inc., Rahway, NJ, USA, also known as Merck Sharp & Dohme LLC, Rahway, NJ, USA, does not accept unsolicited assistance from search firms for employment opportunities. All CVs / resumes submitted by search firms to any employee at our company without a valid written search agreement in place for this position will be deemed the sole property of our company.  No fee will be paid in the event a candidate is hired by our company as a result of an agency referral where no pre-existing agreement is in place. Where agency agreements are in place, introductions are position specific. Please, no phone calls or emails. 

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Flexible Work Arrangements:

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