Workbench.
Free tools that run entirely in your browser. Nothing you paste is uploaded. Each page explains the equations, the assumptions and the references.
T-01Molecular dynamics GROMACS .mdp checker Paste an .mdp file and get grompp-style errors, warnings and fixes, or build EM/NVT/NPT/MD templates. Open tool → SAMPLE · broken NPT, CHARMM36 innpt.mdp · 23 linesout2 errors · 3 warningsoutgrompp would stop on 2 errors T-02Binding & assays IC50 → Ki converter Cheng–Prusoff for competitive, noncompetitive, uncompetitive, mixed and binding assays, with tight-binding checks. Open tool → SAMPLE · Cheng–Prusoff, competitive inIC50 120 nM · [S] 10 µM · Km 5 µMoutKi 40 nM T-03Binding & assays Kd ↔ ΔG + ligand efficiency Convert Kd, Ki or IC50 to binding free energy at any temperature, and compute LE, LLE and BEI. Open tool → SAMPLE · 1 M standard state inKd 10 nM · 298.15 KoutΔG° −10.91 kcal/mol T-04Docking Vina box generator Paste a PDB, pick residues or a ligand, get center/size, a Vina config file and a Python snippet. Open tool → SAMPLE · 1HSG, ligand MK1 incrystal ligand · 5 Å paddingoutcenter 11.634 22.470 5.859outsize 24.854 × 20.214 × 18.635 Å