Represent the chemistry
Force-field parameterization for non-standard systems, informed by quantum-mechanical calculations.
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Molecular modeling for the hard cases.
Founded by Professor Kyle Koss, Peptide Dynamics brings together specialist molecular modeling, custom scientific instrumentation, and practical quality and regulatory support.
Our scientific foundation
Scientific expertise.
Practical development.
Founded by Professor Kyle Koss, Peptide Dynamics brings together specialist molecular modeling, custom scientific instrumentation, and practical quality and regulatory support.
Where we come in
When AI structure prediction isn’t enough.
For the chemistry, environment, and dynamics that a structure alone does not resolve.
01 / MOLECULAR MODELINGCustom force fields.
Custom force fields.
The details matter.
When standard parameters do not adequately represent your system, the simulation needs a more considered starting point.
Build the molecular environment
Model proteins with ligands, cofactors, membranes, or nucleic acids around the question being investigated.
Investigate the behavior
Use atomistic simulation, trajectory analysis, and binding-energy calculations to examine the system beyond its starting structure.
Write up the findings
Where agreed in scope: computational methods, results, and figures drafted as a manuscript section, interpreted alongside your experimental data, for you and your co-authors to revise.
What your project can include
System preparation, custom force-field parameters, simulations, and analysis, through to a draft manuscript section: computational methods, results, and figures, interpreted alongside your experimental work. Your proposal defines the report, figures, any manuscript drafting, and agreed data or reproducibility files, together with assumptions and limitations.
Selected modeling capabilities
Complexity takes
different forms.
Examples from our modeling portfolio.
Each system starts with a different scientific question.
Non-standard chemistry
Metal coordination, iron–sulfur clusters, and heme-containing systems.
Interactions in context
Protein–ligand, protein–protein, and protein–DNA systems, including membrane environments.
Beyond conventional targets
Protein–gold nanoparticle systems and boron-nitride nanotube simulations.
02 / Scientific instrumentation
Custom systems, thoughtful upgrades,
and the connections that make them work.
Instrumentation
built around
your experiment.
A research question can demand more than an off-the-shelf setup. We help define, adapt, and integrate the hardware and software your experiment needs.
From legacy microscope upgrades to custom measurement systems, our work connects equipment choices with the data you need to collect.
FROM REQUIREMENT TO READOUT
- 01
Define the experiment
Measurement needs, existing equipment, and practical constraints.
- 02
Connect the system
Hardware selection, interfaces, and instrument-control software.
- 03
Test the readout
Performance checks, data analysis, and documented limitations.
Hardware + Software + Scientific context
Selected project experience
Defined scopes. Concrete deliverables.MICROSCOPE MODERNIZATION
A clearer path
to an imaging upgrade.
Assessment of a legacy calcium-imaging microscope, definition of functional requirements, and selection of compatible equipment and software.
Illustrative
DELIVERED
Equipment recommendations and vendor coordination to support procurement.
MICROFLUIDIC MEASUREMENT
Making sense of
prototype impedance data.
Data quality checks, frequency-dependent analysis, and technical characterization of fixed-cell measurements from a prototype microfluidic impedance system.
Illustrative
DELIVERED
Consolidated analysis and recommendations. Live-cell validation remained a next step.
Installation, integration, testing, and end-user training can be scoped around your laboratory and project requirements.
Supporting your development
Quality systems
for your next stage.
Practical quality and regulatory support for early-stage companies, startups, and small businesses.
Build the processes and documentation your team needs as your product and operations develop. We help you identify priorities and define a manageable scope.
- Quality management systems and documentation
- Supplier qualification and manufacturing support
- Audit readiness and regulatory planning
Client experience
Peptide Dynamics’ molecular modelling work and final report exceeded our expectations. We are grateful to the entire team for their expertise, responsiveness, and genuine scientific engagement throughout the project.
Our experience working with Peptide Dynamics was fantastic. Their expertise helped us address complex scientific questions, and the time they devoted to explaining the methods and discussing the results added real value to our research.
Publications
Our papers
and preprints.
Papers, preprints and manuscripts that include work by Peptide Dynamics scientists. A work is listed once it names Peptide Dynamics and our collaborators agree.
Featured · bioRxiv · September 2026 · Preprint
Investigating
TRPC6–caveolin-1
interactions.
A study co-authored by researchers affiliated with Peptide Dynamics combines all-atom molecular dynamics with binding-energy analysis to examine this protein–protein interface.
Peptide Dynamics is listed as an affiliation for Shayesteh Bazsefidpar and Kyle M. Koss.
Read the preprintBazsefidpar et al. · Posted September 10, 2026
doi: 10.64898/2026.09.09.750526
This version has not yet been peer reviewed.
All publications
Atomistic Insights into TRPC6–Caveolin-1 Interactions Interface via All-Atom Molecular Dynamics Simulations: Structural and Energetic Basis for Selective Modulation
Bazsefidpar S., Mori M. X., Mosadeghi H., Israni A. K., Koss K. M., Polat O. K.
bioRxiv · doi: 10.64898/2026.09.09.750526 · Peptide Dynamics affiliation
Preprints have not yet been peer reviewed. Listing a publication does not imply endorsement by the authors' institutions.
Ways to work together
A defined question
Focused project
- A modeling study, instrument assessment, or quality-system review.
- Agreed deliverables and a defined scope.
- A proposal setting out costs, assumptions, and exclusions.
A developing program
Ongoing support
- Specialist input across a sequence of research or development milestones.
- Priorities reviewed as the work develops.
- Coordination, technical reviews, and agreed next steps.
Questions before we start
Grouped by service: molecular modeling, scientific instrumentation, quality & regulatory, then getting started.
We work on protein–ligand, protein–protein, membrane, and nucleic-acid systems, including non-standard chemistry such as metal coordination sites and cofactors. We review the scientific question and available inputs before proposing a method.
Beyond simulations and analysis, we can draft the computational methods, results, and figures as a manuscript section, interpreted alongside your experimental data and ready for you and your co-authors to revise. The proposal defines the report, figures, any manuscript drafting, and agreed data or reproducibility files, together with assumptions and limitations. Authorship or acknowledgement is agreed with you at the outset.
AI can support selected stages of molecular modeling, including structure prediction. We choose methods around the scientific question and assess their limitations alongside simulation and experimental evidence.
When using external AI services, we select business plans with contractual data protection appropriate to the project’s confidentiality requirements. For projects requiring stricter control, we offer locally hosted AI models running on our own computing infrastructure, on our premises. Where suitable for the agreed workflow, this allows confidential project data to be processed without sending it to external AI providers. We agree on confidentiality and data residency requirements before work begins.
Yes. An instrumentation engagement can start with a review of the current setup, measurement requirements, and hardware or software constraints. We then scope equipment selection, integration, testing, or training as appropriate.
Both, depending on the measurement problem. Where standard equipment does not fit, we can design and integrate a custom measurement setup around your experimental requirements. The proposal defines what is built, tested and handed over.
We start with your product, development stage, intended market, and existing processes. Together we identify the documentation, quality-system, supplier, or readiness work that is appropriate for your team.
Yes. We can start from little or no existing documentation and build the procedures and records appropriate to your stage. We help you prepare for audits; certification itself is issued by the relevant certification body.
Share the question you need to answer, your current setup or data, and your timing constraints. We review the fit and define the deliverables, inputs, costs, and schedule in a project proposal.
About Peptide Dynamics
Who we are.
How we started.
A specialist scientific consultancy: molecular modeling, scientific instrumentation, and practical quality and regulatory support.
Professor Kyle Koss
Founder, Peptide Dynamics
Peptide Dynamics was founded by Professor Kyle Koss, whose research spans peptide engineering, biomaterials, and neuroinflammation.
We combine this scientific foundation with expertise in molecular modeling, scientific instrumentation, and quality systems to help clients move from research questions toward practical development.