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<p>Mixed-solvent molecular dynamics (MSMD) has become a useful simulation strategy for mapping protein interaction hotspots, exploring cryptic or allosteric pockets, and characterizing ligandable surface regions. However, practical MSMD studies still require labor-intensive system preparation, probe bookkeeping, format conversion, and trajectory post-processing across multiple software environments. Here, we present the Mixed-Solvent MD Suite, a modular software platform that automates these operational steps rather than proposing a new physical sampling formalism. The Suite includes (1) a fully web-based Mixed Solvent MD System Builder for protein and probe setup, concentration-controlled solvation (% w/v or mol/L), and automated generation of GROMACS and AMBER compatible input files, and (2) a local Probe GridMap Builder for grid-based probe occupancy analysis of MD trajectories using the AMBER cpptraj backend. Case studies on five benchmark proteins show that the platform reproducibly constructs MSMD systems, supports transferable analysis workflows across simulation outputs, and qualitatively recovers known ligandable regions in representative targets. Overall, the Mixed-Solvent MD Suite lowers technical barriers for MSMD studies and provides an extensible foundation for future benchmarked hotspot analysis and cryptic-site discovery workflows.</p>

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Mixed-Solvent MD suite: modular tools for building and analyzing mixed-solvent molecular dynamics systems

  • 期刊论文

  • 发表日期：

    2026年5月25日

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  • Qiu Yue,
  • Liu Qing,
  • Xie Jian-Wu

摘要

Mixed-solvent molecular dynamics (MSMD) has become a useful simulation strategy for mapping protein interaction hotspots, exploring cryptic or allosteric pockets, and characterizing ligandable surface regions. However, practical MSMD studies still require labor-intensive system preparation, probe bookkeeping, format conversion, and trajectory post-processing across multiple software environments. Here, we present the Mixed-Solvent MD Suite, a modular software platform that automates these operational steps rather than proposing a new physical sampling formalism. The Suite includes (1) a fully web-based Mixed Solvent MD System Builder for protein and probe setup, concentration-controlled solvation (% w/v or mol/L), and automated generation of GROMACS and AMBER compatible input files, and (2) a local Probe GridMap Builder for grid-based probe occupancy analysis of MD trajectories using the AMBER cpptraj backend. Case studies on five benchmark proteins show that the platform reproducibly constructs MSMD systems, supports transferable analysis workflows across simulation outputs, and qualitatively recovers known ligandable regions in representative targets. Overall, the Mixed-Solvent MD Suite lowers technical barriers for MSMD studies and provides an extensible foundation for future benchmarked hotspot analysis and cryptic-site discovery workflows.