RUN-BIO-022Biomedical & Clinical Audited on 2026-10-04• Version 2026.10-v1

Reverse Vaccinology & mRNA Design Against Antimicrobial Resistance (AMR)

Evaluated Benchmark Prompt

"What are the most validated computational pipelines combining machine learning antigen prediction with mRNA sequence optimization for Gram-negative ESKAPE pathogens?"

Replication Protocol: Evaluated against peer-reviewed bacteriology literature (Nature Reviews Microbiology, Frontiers in Immunology). Audited candidate targets: outer membrane proteins, siderophore receptors, and secretion systems.

Empirical Tool Evaluations (2)

Audited against CrossRef & PubMed APIs

Research Assistant Pro (DeepResearcher)

Publisher Tool

Autonomous multi-hop academic synthesis with inline DOI verification

Citation Rate94.7%

Latency 58s

Verified / Total18 / 19

Synthesized Output Excerpt

Modern RV 2.0 pipelines integrate Vaxign-ML and NetMHCpan-4.1 with mRNA codon optimization algorithms (such as LinearDesign for minimum free energy mRNA secondary structure). For Pseudomonas aeruginosa and Acinetobacter baumannii, primary validated targets include OmpA, BamA, and outer membrane iron transport complexes (FpvA).

Auditor Notes: 18 peer-reviewed citations verified. Accurately detailed the LinearDesign dynamic programming algorithm and in vivo murine challenge data.

Line-by-Line DOI Verification Logs (1 audited)

Verified DOILinearDesign: Efficient mRNA design with optimal structure and codon usage

View DOI / Paper

Claim Made"LinearDesign jointly optimizes mRNA half-life and protein translation efficiency."

Ground Truth Paper Excerpt"Dynamic programming computes optimal mRNA sequences balancing structural stability and codon adaptation index."

Scite.ai

Smart Citations showing whether research papers are supported or contrasted

Citation Rate93.3%

Latency 32s

Verified / Total14 / 15

Synthesized Output Excerpt

Computational reverse vaccinology identifies surface-exposed virulence factors. Vaxign and Jenner-pc pipelines identify TonB-dependent receptors as candidate epitopes, with 12 independent studies confirming protection in animal sepsis models.

Auditor Notes: Smart Citations identified 3 contrasting citations noting difficulties in folding multi-pass transmembrane beta-barrel proteins.

Line-by-Line DOI Verification Logs (1 audited)

Verified DOIMachine Learning for Reverse Vaccinology: A Systematic Review

View DOI / Paper

Claim Made"Benchmarking antigenicity prediction tools on bacterial pathogens."

Ground Truth Paper Excerpt"Vaxign-ML improves predictive precision over classic threshold heuristics."

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