One Blob to Rule Them All: A Universal Dual-Topology Nonequilibrium Framework for Relative and Absolute Binding Free Energies via a Lennard-Jones Blob Reference

Essential data for reproducing the results from "ONE BLOB TO RULE THEM ALL: A UNIVERSAL DUAL-TOPOLOGY NONEQUILIBRIUM FRAMEWORK FOR RELATIVE AND ABSOLUTE BINDING FREE ENERGIES VIA A LENNARD-JONES BLOB REFERENCE"ABSTRACT: Single-topology free energy perturbation (FEP) methods, while accurate for congeneric series, require chemical similarity between ligands, bespoke perturbation networks, and offer no direct route to absolute binding free energies (ABFEs). Here we introduce DT-NE-Alchemy, a dual-topology nonequilibrium (NE) framework that eliminates these constraints through a universal Lennard-Jones (LJ) blob reference state. The LJ blob—a minimal, rigid molecule (as small as a single LJ particle) designed to fit the binding pocket—serves as a common anchor for alchemical transformations. Relative binding free energies between any two ligands are obtained by two-edges transformations L_i -> L_j, yielding all n(n-1)/2 pairwise values from only n blob-based calculations. Crucially, ABFEs follow directly as DG_blob + DDG_blob -> L_i, converting the long-sought "holy grail" of computational drug design into a practical reality. Applied to 16 MCL-1 ligands spanning indole, benzothiophene, and benzofuran scaffolds, the method achieves Pearson correlations up to 0.88, Kendall up to 0.80, and mean unsigned errors of 1.2-1.5 kcal/mol for 120 relative pairs. The methodology delivers credible, tunable confidence intervals directly from BAR analysis - controllable via switching time tau and trajectory count N - without costly replicate simulations. All computational tasks are embarrassingly parallel, perfectly aligned with leadership-class HPC systems. DT-NE-Alchemy is program-agnostic, automatable, and poised to replace FEP+ as the workhorse for scalable, physically grounded binding free energy calculations in AI-driven drug discovery.Directory tree:├── ABFE_blobs│   ├── blb6│   ├── blobs│   ├── data_abs│   │   ├── abcg2│   │   │   └── TABLES│   │   └── am1bcc│   │       └── TABLES│   └── Datap├── bin├── doc├── pdb├── RBFE│   ├── ABCG2│   │   ├── data│   │   │   └── TABLES│   │   ├── Datarel│   │   ├── lib│   │   └── vdssb│   ├── AM1BCC│   │   ├── data│   │   │   └── TABLES│   │   ├── Datarel│   │   ├── lib│   │   └── vdssb│   ├── gplt│   ├── input_examples│   │   ├── HREM│   │   └── NE│   │       ├── b-pdbs│   │       └── u-pdbs│   └── NE-paths└── zipABFE_blobs: results for ABFE using blobs as referencebin: contains ancillary scriptsdoc: contains the paper preprint "One Blob to Rule Them All: A Universal  Dual-TopologyNonequilibrium Framework for Relative and Absolute Binding FreeEnergies via a Lennard-Jones Blob Reference" pdb: contains the PDB files for the MCL-1 ligands.RBFE: results for RBFEszip: contains the latest orac.6_3.tar.gz ORAC distribution (for installation instructions see www1.chim.unifi.it/orac ) . More info inside each directory.