From sequence to scientific decision

MDL is designed for researchers, molecular biologists, biotechnologists, immunologists, laboratory scientists and students working with sequence-based molecular research workflows.

Current workflows include primer and RT-qPCR design, assay assessment, peptide analysis, MHC/HLA prediction, molecular and vector design, project workflows and scientific reporting.

No. Calculated properties and computational predictions should be interpreted in their biological context and experimentally validated where appropriate.

Compatible MDL tools are designed to support connected workflows so that biological context, design parameters, selected candidates and reporting information can move between relevant stages.

Several MDL workflows support structured scientific reports or exports that preserve selected results, design parameters and relevant interpretation context.

MDL uses distinct terms for different kinds of information. A calculated property is derived directly from supplied data or a defined formula. A computational prediction is a model- or rule-based estimate. A researcher decision records a documented human choice within the workflow. Experimental evidence comes from laboratory or other independently generated observations. These categories should not be treated as equivalent.

Captured means that the item is documented in the current research snapshot. It does not mean experimentally validated or scientifically confirmed. Missing means the item is not documented in the current snapshot; it does not by itself mean the evidence does not exist elsewhere.

Some workspace features, including Run History, reliability logs and recovery checkpoints, use storage in this browser. Recovery checkpoints may contain the complete active research snapshot, including biological sequences or other research content. Browser-local storage is not a cloud or institutional backup. Export data that must be retained, and review the applicable data-handling conditions before sending confidential or sensitive information to any external service.

Start with the scientific question and the type of input you already have. Use Design Assay for assay planning, Primer Design or RT-qPCR for sequence-based primer design, Variant → Experiment for a defined variant, Batch VCF or Cohort Analysis for variant sets, Protein Sequence Analyzer or Protein → Peptide Designer for protein-derived workflows, and the User Guide when you are unsure which route fits your task.

Yes. Restriction Enzyme Analyzer maps recognition and cut sites and predicts digest fragments from a supplied DNA sequence. Virtual Gel Electrophoresis can then be used to visualize expected fragment separation. These are computational planning tools; enzyme conditions and experimental gel behavior should still be checked independently.

Protein Sequence Analyzer helps inspect sequence properties and annotated sequence features. Protein → Peptide Designer generates peptide windows for downstream screening, while Peptide Analysis evaluates candidate-level properties. Selected peptides can be carried into relevant MHC/HLA workflows. Computationally attractive candidates are not evidence of biological activity.

MHC / HLA Prediction prioritizes peptide candidates using predicted binding to supported human HLA or mouse MHC targets. Binding predictions are screening evidence only: they do not by themselves establish antigen processing, presentation, immunogenicity or an experimental immune response.

Population Coverage estimates HLA coverage from supplied epitope-to-HLA restrictions and a cited population allele-frequency dataset. The result depends on the supplied frequencies, represented alleles and model assumptions. Missing alleles are not evidence of zero frequency, and modeled population coverage is not an individual-level prediction.

CRISPR Guide Designer ranks candidate guides from a user-supplied DNA sequence using transparent sequence-level checks and the selected nuclease context. Candidate ranking supports research planning but does not establish editing efficiency, specificity or biological outcome. Selected guides should be independently evaluated and experimentally validated.

Provenance & Evidence helps review the active research snapshot for source context, accessions, datasets, methods, versions, parameters, warnings and other traceability information. Better provenance improves reproducibility and review, but provenance completeness does not prove scientific, clinical or regulatory validity.

No. MDL can calculate, predict, compare and organize candidate information, but candidate selection remains a researcher decision. Scientific Decision is designed to keep compared candidates, warnings, provenance and the researcher's rationale visible rather than silently converting a score into a scientific conclusion.

Preserve the relevant input context, accession or reference sequence, important parameters, method or database information when available, warnings, selected outputs and retrieval or analysis date. Scientific Report, Run History, Project Workspace, Provenance & Evidence and export functions can help retain this context. Keep independent copies when a durable institutional research record is required.

No. Molecular Design Lab is intended for research workflows. Computational predictions, design candidates, workflow-completeness records and software-generated reports do not establish clinical validity, diagnostic performance, treatment suitability or regulatory compliance.