ASAP Jobs

Seeking talented scientists for the open science ASAP antiviral discovery center

Open positions

Researcher in large-scale alchemical free energy calculations and structure-based machine learning to drive open science antiviral discovery programs

Postdoctoral Research Scholar or Research Associate
Memorial Sloan Kettering Cancer Center | Remote or NYC
Duration: Up to five years
ASAP Investigator: John Chodera
Apply: [application link]
Contact: apply@choderalab.org

The Chodera lab is using alchemical free energy calculations and structure-informed machine learning methods to aid the open science ASAP antiviral drug discovery (AViDD) Center in aiding the medicinal chemistry team by prioritizing small molecules for synthesis based on affinity, selectivity, robustness to mutations, and other ADMET properties. Scientists working on the project will help develop, run, interpret, and systematically improve large-scale calculations on Folding@home and other GPU-accelerated computing resources as part of a large, distributed, open science drug discovery Center that will initially focus on the discovery of direct-acting oral antivirals with the aim of global equitable and affordable access. The Researcher role will help drive both applications and methodological advances that support structure-enabled hit expansion (Project 2), hit-to-lead (Project 3), and lead optimization (Project 5) aspects of the project, working closely with both the Data Core and medicinal chemists to automate as much as possible. This is an amazing opportunity to develop open source software, develop and assess new predictive algorithms that are rapidly tested experimentally in the service of open antiviral drug discovery, and to contribute to the discovery of new therapeutics aimed at global, equitable, and affordable access.

What we’re looking for:

Someone with experience with alchemical free energy calculations and/or structure-informed machine learning methods (such as e3nn)
Someone with an aptitude for Python
You speak Python at a level where you are comfortable writing classes with inheritance, your own decorators and context managers, and parameterized unit tests.
Experience with GitHub as a means of collaborative software development
You have a passion for working together with other software developers, software scientists, and scientists to make awesome, usable tools for science; we work closely with organizations like the Molecular Sciences Software Institute (MolSSI) to jointly develop software best practices (see our own best practices and MolSSI’s ) to better enable the community to collaborate and to ensure our students and postdocs are familiar with best practices used in industry
You are excited to collaborate with other organizations like Folding@home, the Open Force Field Initiative, the Drug Design Data Resource (D3R), and the Molecular Sciences Software Institute (MolSSI), and other AViDD Centers
You possess a good measure of patience in working with a variety of different kinds of people
You’re excited about contributing to some amazing scientific initiatives in open science, drug discovery, and open source software to enable this
You can ensure at least a few key hours of your workday overlap normal NYC working hours (M-F 10-5)

Other bonus (but certainly not required!) experience:

Experience with OpenMM and the OpenMM ecosystem is a huge plus
You have any exposure to the concepts or tools of Markov chain Monte Carlo, since a lot of our algorithms are based on these concepts
Familiarity with, or a desire to learn, aspects of medicinal chemistry for small molecule drug discovery

Software Scientist to support large-scale alchemical free energy calculations and structure-based machine learning to drive open science antiviral discovery programs

Software Scientist
Memorial Sloan Kettering Cancer Center | Remote or NYC
Duration: Up to five years
ASAP Investigator: John Chodera
Apply: [application link]
Contact: apply@choderalab.org

The Chodera lab is using alchemical free energy calculations and structure-informed machine learning methods to aid the open science ASAP antiviral drug discovery (AViDD) Center in aiding the medicinal chemistry team by prioritizing small molecules for synthesis based on affinity, selectivity, robustness to mutations, and other ADMET properties. Scientists working on the project will help develop, run, interpret, and systematically improve large-scale calculations on Folding@home and other GPU-accelerated computing resources as part of a large, distributed, open science drug discovery Center that will initially focus on the discovery of direct-acting oral antivirals with the aim of global equitable and affordable access. The Software Scientist role will help develop both next-generation molecular simulation, free energy calculation, and structure-informed machine learning infrastructure—including next-generation molecular modeling engines in differentiable modeling frameworks like JAX and PyTorch—and help build infrastructure to support structure-enabled hit expansion (Project 2), hit-to-lead (Project 3), and lead optimization (Project 5) aspects of the project, working closely with both the Data Core and medicinal chemists to automate as much as possible. This is an amazing opportunity to develop open source software, develop and assess new predictive algorithms that are rapidly tested experimentally in the service of open antiviral drug discovery, and to contribute to the discovery of new therapeutics aimed at global, equitable, and affordable access.

What we’re looking for:

Someone with an aptitude for Python, and potentially also C++/CUDA/OpenCL
You speak Python at a level where you are comfortable writing classes with inheritance, your own decorators and context managers, and parameterized unit tests.
Your IDE is configured with modern tooling like black autoformatting, pylint, and AI-assisted autocompletion
We make extensive use of git and GitHub: branches, forks, PRs, rebasing, cherry-picking are not foreign concepts to you
Your exploratory work happens in notebooks and you like when they look pretty
Code reviews do not sound scary but exciting
You have a passion for working together with other software developers, software scientists, and scientists to make awesome, usable tools for science; we work closely with organizations like the Molecular Sciences Software Institute (MolSSI) to jointly develop software best practices (see our own best practices and MolSSI’s ) to better enable the community to collaborate and to ensure our students and postdocs are familiar with best practices used in industry
You are excited to collaborate with other organizations like Folding@home, the Open Force Field Initiative, the Drug Design Data Resource (D3R), and the Molecular Sciences Software Institute (MolSSI)
You possess a good measure of patience in working with a variety of different kinds of people
You’re excited about contributing to some amazing scientific initiatives in open science, drug discovery, and open source software to enable this
You can ensure at least a few key hours of your workday overlap normal NYC working hours (M-F 10-5)

Other bonus (but certainly not required!) experience:

You have experience with machine learning frameworks (where autodiff and JIT compilation are native) such as JAX, PyTorch, or TensorFlow
You have experience with alchemical free energy calculations and/or structure-based machine learning methods (such as e3nn)
You have experience with biomolecular simulation theory and/or simulation packages (especially OpenMM) is a huge plus
You have Python packaging experience with conda, which makes it easy to deploy tools and their dependencies (including GPU-accelerated tools). Huge bonus points if you’ve contributed to the fantastic packaging ecosystem conda forge, or also have experience with pip.
You have enough CI experience to be excited by GitHub Actions. Green check marks make you happy.
You have any exposure to the concepts or tools of Markov chain Monte Carlo, since a lot of our algorithms are based on these concepts
You have a degree (BS, PhD) in the physical or biosciences or computer-focused discipline, but this is certainly not required
You have some experience with cloud dev ops (e.g. AWS EC2, S3, AWS Batch) is a plus, since we’re starting to migrate some Folding@home workflows there

Researcher in design of compounds and coordination of design-make-test-analyse cycle to drive antiviral discovery programs

Medicinal Chemist
MedChemica Consultancy Ltd | United Kingdom
Duration: 1 year initial contract with opportunity for further permanent position
ASAP Investigator: Dr. Ed Griffen
Contact: contact@medchemica.com

MedChemica is leading the optimization of new antiviral agents within the ASAP antiviral drug discovery (AViDD) Center. Within our team, we analyse biological and ADMET testing data, and combine that with protein-ligand structural data, FEP calculations and machine learning methods to both design and prioritise compounds for synthesis. As a member of the lead optimization team, you will work closely with teams of synthetic chemists, other medicinal chemists, computational chemists, virologists, pharmacokineticists and physical chemists to make sure the best compounds get made and tested. The lead optimization team is central in delivering the overall Center goals of generating new anti-virals for human trials ready to treat future pandemics. You will be working within MedChemica Consultancy Limited where you will be a supportive and supported team member, and where you will also have opportunities to contribute to the development of new AI tools for medicinal chemistry.

What we’re looking for:

With a PhD and /or post doctoral experience in medicinal, synthetic or physical organic chemistry, you are confident in relating organic chemical structures to their properties and synthesis,
A desire to learn medicinal chemistry for small molecule drug discovery,
An interest in learning virology and human biology in order to work with our biology and ADMET colleagues,
An enthusiasm to apply modern methods in computational chemistry to accelerate drug discovery,
Great team working skills for collaborating with a huge range of diverse, highly talented scientists across the globe,
You are UK based and have the right to work in the UK,
We offer flexible working arrangements, but you will be expected to be able to spend at least 3 days per week in our office located in Macclesfield town centre, Cheshire.

Other bonus (but certainly not required!) experience:

Experience in working in interdisciplinary and cross-cultural environments

To coordinate structure biology support and structural enablement across projects and cores

Computational Chemistry Postdoctoral Research Associate
Diamond Light Source | Oxford
Duration: Up to 5 years
ASAP Investigator: Frank von Delft
Contacts: frank.von-delft@diamond.ac.uk daren.fearon@diamond.ac.uk

The development of novel, low cost and globally available antiviral therapeutics remains an essential goal for the current SARS-CoV-2 pandemic. Furthermore, future pandemics could be prevented with easily deployable broad spectrum oral antivirals and open knowledge bases that de-risk and accelerate novel antiviral discovery and development.

Structure-enabled drug design and fragment-based drug discovery have made significant contributions to the development of these much-needed antivirals with over 2,000 X-ray crystal structures deposited in the Protein Data Bank to date. Facilities like the XChem fragment screening platform at Diamond have enabled efforts such as the COVID Moonshot – a fully open-science structure-enabled drug discovery campaign targeting the SARS-CoV-2 main protease that developed a pre-clinical candidate targeting the SARS-CoV-2 Main protease in less than 2 years.

As part of a new NIH funded Antiviral Drug Discovery (AViDD) Center for Pathogens of Pandemic Concern we are seeking to recruit enthusiastic crystallographers, technicians, informaticians and a research coordinator to deliver high-throughput fragment screening experiments and rapid structural support for hit-to-lead development of novel inhibitors targeting SARS-CoV-2 and other viruses. The appointed people will work closely with the XChem and I04-1 teams as well as an international collection of collaborators.

A computational chemistry PDRA will be responsible for driving and completing first round follow-up of all XChem screening campaigns. This will entail performing the computational and intellectual work for designing and finalising lists of candidate compounds; sourcing them from vendors, in particular Enamine, assisted by Center partner PostEra; and designing and executing the robot-based synthesis experiments already being developed at Diamond in partnership with the Rosalind Franklin Institute and the EUbOPEN IMI2 project. The tapered effort reflects the tapered outputs envisioned for Project 2; the person will at that point be assigned to additional projects, and co-funded accordingly.

Conduct world-leading research aligned to delivering successful crystallographic (XChem) fragment screens and rapid turn-around of protein-ligand crystal structures to enable hit-to-lead development of novel anti-virals.

Postdoctoral Research Associate
Diamond Light Source | Oxford
Duration: Up to 5 years
ASAP Investigator: Frank von Delft
Contacts: frank.von-delft@diamond.ac.uk daren.fearon@diamond.ac.uk

In this role, you will:

Be responsible for delivering successful crystallographic (XChem) fragment screens and rapid turn-around of protein-ligand crystal structures to enable hit-to-lead development.
Ensure all crystal structures are promptly available, at high quality and fully annotated, in the public domain.
Develop and test new and existing methodologies to increase the throughput of the XChem platform.
Report to the project supervisor, you will contribute to the on-going research within the group.
Be responsible for carrying out work to fulfil the aims of the research proposal detailed in the Job Description appendix.
Manage the day-to-day running of a research project.
Identify research objectives and carry out appropriate research activities within a given timescale.
Attend internal scientific and administrative meetings with scientific collaborators.
Lead in the analysis and authoring of scientific results in international peer-reviewed journals.
Keep up with latest results and international research directions, especially in interest for the research project associated with this post.

About you

You will have an appropriate Science Degree (Biochemistry/Chemistry/Chemical Biology) and an appropriate PhD together with proven relevant experience. You will also need to be able to communicate and interact with staff on all levels with good organisation skills and the ability to work flexibly. First-hand experience in crystallographic fragment screening and compound development is highly desirable.

The successful candidate will likely have:

An interest in protein crystallography and drug discovery, particularly fragment-based drug discovery or structure-based drug design
Strong analytical skills and excellent record keeping
Good organisational and time management skills

To provide support to anti-viral research at the XChem facility and assist with the delivery of successful crystallographic (XChem) fragment screens and rapid turn-around of protein-ligand crystal structures.

Research Assistant
Diamond Light Source | Oxford
Duration: Up to 5 years
ASAP Investigator: Frank von Delft
Contacts: frank.von-delft@diamond.ac.uk daren.fearon@diamond.ac.uk

In this role, you will:

Provide general laboratory support to the XChem facility and upkeep the operation of equipment.
Assist with the delivery of successful crystallographic (XChem) fragment screens and rapid turn-around of protein-ligand crystal structures.
Contribute to the development and testing of new and existing methodologies to increase the throughput of the XChem platform.
Reporting to the project supervisor, you will contribute to the on-going research within the group.
Keep up with latest results and international research directions, especially in interest for the research project associated with this post.

About you

You will have an appropriate Science Degree and an appropriate PhD together with proven relevant experience. You will also need to be able to communicate and interact with staff on all levels with good organisation skills and the ability to work flexibly. Experience in fragment-based drug discovery will be advantageous.

The successful candidate will likely have:

An interest in high-throughput protein crystallography and fragment-based drug discovery
Excellent organisational and time management skills
Good laboratory practice

To coordinate structure biology support and structural enablement across projects and cores.

Research Coordinator
Diamond Light Source | Oxford
Duration: Up to 5 years
ASAP Investigator: Frank von Delft
Contacts: frank.von-delft@diamond.ac.uk daren.fearon@diamond.ac.uk

A scientific coordinator PDRA with background in drug discovery, biochemistry or chemistry, will be tasked with implementing and delivering scientific project management, exploiting Diamond’s processes for technical projects. This role is crucial in view of the many contributors involved in delivering even one enabled target, a lesson adopted from the Wellcome-funded TEP grant (2015-2020) in Oxford. Scientific expertise is crucial, as the role encompasses dissemination of outputs, including capturing Project 2 outcomes in scientific papers.

Researcher in antiviral drug discovery for RNA viruses of pandemic potential

Postdoctoral Associate
Icahn School of Medicine at Mount Sinai | NYC, New York
Duration: Up to 5 years
ASAP Investigator: Kris White
Apply: [application link]
Contact: kris.white@mssm.edu

A Postdoctoral Associate position is immediately available in the Microbiology Department in the Icahn School of Medicine at Mount Sinai in the laboratory of Dr. Kris M. White as part of a multi-disciplinary program focused on the development of clinic-ready orally-bioavailable antiviral drugs for the treatment of viruses with pandemic potential, particularly influenza A virus, picornaviruses, flaviviruses, and coronaviruses. The goal of the project is to develop effective antiviral drugs that can be deployed at the earliest stages of the next viral pandemic, with the potential of saving millions of lives. This position will be focused on using high throughput screening approaches, animal models for antiviral development, and advanced approaches to analyze antiviral resistance patterns using next generation sequencing methods. The person filling this position will play an important intellectual, technical, and scientific role in leading these projects. Position is supported by NIH funding through Antiviral Drug Discovery (AViDD) centers.

Primary Responsibilities:

Independent experimental designs and data analysis
Carries out a wide range of molecular virology and biochemistry techniques
Accurately documents experiments and data
Contributes to writing of reports and manuscripts with increasing responsibility over time
Works collaboratively across lab functions and train other junior lab staff as needed

Required Experience:

Ph.D. degree in biological science is required
Strong background in virology, molecular biology, and biochemistry
Experience working with viruses is required
BSL-3 experience is a plus

Knowledge, Skills, and/or Abilities:

Demonstrated knowledge in relevant specialized disciplines
The ability to work independently and to handle multiple projects and deadlines
Demonstrated ability to work in an interactive and collaborative team
Excellent presentation, verbal, and written communication skills
Possess strong attention to detail, analytical, time management, organizational, and interpersonal skills
Embody the Institute’s core values of Commitment, Collaboration, Communication, Community and Compassion

Researcher in antiviral drug discovery for RNA viruses of pandemic potential

Research Associate
Icahn School of Medicine at Mount Sinai | NYC, New York
Duration: Up to 5 years
ASAP Investigator: Kris White
Apply: [application link]
Contact: kris.white@mssm.edu

A Research Associate position is immediately available in the Microbiology Department in the Icahn School of Medicine at Mount Sinai in the laboratory of Dr. Kris M. White as part of a multi-disciplinary program focused on the development of clinic-ready orally-bioavailable antiviral drugs for the treatment of viruses with pandemic potential, particularly influenza A virus, picornaviruses, flaviviruses, and coronaviruses. The goal of the project is to develop effective antiviral drugs that can be deployed at the earliest stages of the next viral pandemic, with the potential of saving millions of lives. This position will be focused on using high throughput screening approaches, animal models for antiviral development, and advanced approaches to analyze antiviral resistance patterns using next generation sequencing methods. The person filling this position will play an important intellectual, technical, and scientific role in these projects. Position is supported by NIH funding through Antiviral Drug Discovery (AViDD) centers.

Primary Responsibilities:

Carries out experimental designs and data analysis
Carries out a wide range of molecular virology and biochemistry techniques
Accurately documents experiments and data
Contributes to writing of reports and manuscripts with increasing responsibility over time
Works collaboratively across lab functions and train other junior lab staff as needed

Project Coordinator to support ASAP Antiviral Discovery Center

Project Coordinator
Memorial Sloan Kettering Cancer Center | Remote
ASAP Investigator: John Chodera
Contact: maggie.jameson@choderalab.org

We are seeking a fully remote, independent, and self-motivated project coordinator to oversee complex international scheduling, team communications and coordination, project management platform content and documentation, and every other task that comes up to help establish a new open science drug discovery center with an emphasis on global equitable and affordable access. The international center is composed of geographically distributed team members located across the globe. If you like detail-oriented organization and problem-solving, you’ll excel in this role and learn a lot in the process.

Key responsibilities:

Oversee scheduling operations for a geographically distributed open science drug discovery center that includes members in the United States, Europe, and Asia
Keep team members informed and connected with regular communications and documentation
Independently update project management systems and organizational documentation on a regular basis
Follow up on task lists to ensure that no action item is left behind
Establish efficient operational processes and procedures in coordination with the administrative director
Identify ways that we can be more efficient in everything we do
Partner with scientists and business professionals to achieve scientific and programmatic goals
Help coordinate travel, meetings, and events
Serve as a solution-oriented resource to reduce barriers to scientific progress

Expected qualifications:

Bachelor’s degree in relevant field
Comfortable with technology and software and quick to acclimate to new platforms
High attention to detail with the ability to shift between tasks
Ability to stay motivated and connected with minimal structure
Excellent writing skills