Research Articles
A Practical Framework for Selecting Molecular Dynamics Force Fields in Computational Drug Discovery
This guide provides a comprehensive framework for researchers and drug development professionals to select and validate molecular mechanics force fields.
Explicit vs. Implicit Solvent Models in Molecular Dynamics: A Comprehensive Guide for Computational Researchers
This article provides a comprehensive comparison of explicit and implicit solvent models for molecular dynamics (MD) simulations, tailored for researchers and professionals in computational biophysics and drug development.
Beyond the Noise: Accounting for Homoplasy in ABBA-BABA Tests to Ensure Accurate Introgression Detection
This article addresses a critical challenge in phylogenomic analysis: the confounding effect of homoplasy on the D-statistic (ABBA-BABA test).
Adaptive Introgression: The Genomic Engine of Forest Tree Evolution and Climate Resilience
This article synthesizes contemporary research on adaptive introgression—the natural transfer of beneficial genetic material between species—and its profound impact on forest tree evolution.
Immune-Driven Viral Evolution: From Molecular Mechanisms to Therapeutic Design
This article synthesizes current research on the dynamic interplay between host immune responses and viral evolution, a cornerstone of viral pathogenesis and therapeutic development.
Comparative Phylodynamics for Outbreak Source Attribution: Methodologies, Applications, and Future Directions
This article provides a comprehensive comparison of phylodynamic methods for outbreak source attribution, tailored for researchers and public health professionals.
Validating Phylodynamic Estimates with Epidemiological Data: Methods, Challenges, and Best Practices for Researchers
This article provides a comprehensive framework for validating phylodynamic inferences against epidemiological data, addressing critical needs for researchers and drug development professionals.
Benchmarking AI in Evolutionary Genomics: From Foundational Models to Clinical Impact
This article provides a comprehensive roadmap for researchers and drug development professionals navigating the rapidly evolving field of AI benchmarking in evolutionary genomics.
Navigating the Fitness Landscape: Optimizing Genetic Algorithms for Biomedical Code and Drug Discovery
This article explores the critical role of Genetic Algorithms (GAs) in optimizing solutions for complex, non-differentiable fitness landscapes, with a special focus on applications in drug development and biomedical research.
The Proteomic Constraint: How Protein Demands Shape Genetic Code Evolution and Its Biomedical Implications
This article explores the proteomic constraint hypothesis, a foundational concept proposing that the total size and composition of an organism's proteome exert a primary selective pressure on genetic code evolution.