SurfPotDB — surface electrostatics database (index & README)

SurfPotDB is a database of molecular surface electrostatic potentials computed by solving the continuum Poisson–Boltzmann equation with NextGenPB on structures from the Protein Data Bank (PDB).To avoid redundant calculations, structures extracted from the RCSB Protein Data Bank were grouped into clusters at 90% sequence identity and the electrostatics were computed on one representative per cluster. This release covers 8,571 computed structures (one per sequence cluster), standing for roughly 19,000 PDB entries.Each structure was protonated at pH 7.0 with MCCE4 (maximum-occupancy state) and solved with NextGenPB as a linearized Poisson-Boltzmann calculation (solute dielectric 2, solvent dielectric 80, ionic strength 0.145 M, 298.15 K). For every structure the database provides a surface electrostatic-potential mesh (.vtp: the potential mapped on the molecular surface, enriched with the surface normal and the polarization charge q_pol, so the solution can be reused to reconstruct the potential and field anywhere inside the structure), the protonated structure (.pqr, carrying the per-atom MCCE charges and radii from which the exact pH-7.0 protonation state can be recovered), and an electrostatic energy decomposition (polarization, ionic, Coulombic, total). Energies are in kT and the surface potential in kT/e (about 25.7 mV at 298.15 K); the .vtp opens in ParaView and the .pqr in PyMOL/VMD.This landing record is the citable entry point for the whole database. It contains index.csv (the canonical index: PDB code, energies, surface-potential range, and the Zenodo download URLs of every per-structure .vtp/.pqr file), a static SQLite snapshot for offline querying, and a README listing all shard records with their DOIs. The per-structure files live in companion shard records in the same Zenodo community and are resolved through the URLs in index.csv.Searchable web interface: https://vdiflorio.github.io/surfpotdb/Shard recordsPer-structure .vtp/.pqr files are split across 191 shard records (resolve individual files via the URLs in index.csv): shard 0000 — record 21072016 — DOI 10.5281/zenodo.21072016 (90 files) shard 0001 — record 21072273 — DOI 10.5281/zenodo.21072273 (90 files) shard 0002 — record 21072297 — DOI 10.5281/zenodo.21072297 (90 files) shard 0003 — record 21072328 — DOI 10.5281/zenodo.21072328 (90 files) shard 0004 — record 21072357 — DOI 10.5281/zenodo.21072357 (90 files) shard 0005 — record 21072388 — DOI 10.5281/zenodo.21072388 (90 files) shard 0006 — record 21072423 — DOI 10.5281/zenodo.21072423 (90 files) shard 0007 — record 21072446 — DOI 10.5281/zenodo.21072446 (90 files) shard 0008 — record 21072476 — DOI 10.5281/zenodo.21072476 (90 files) shard 0009 — record 21072507 — DOI 10.5281/zenodo.21072507 (90 files) shard 0010 — record 21072525 — DOI 10.5281/zenodo.21072525 (90 files) shard 0011 — record 21072543 — DOI 10.5281/zenodo.21072543 (90 files) shard 0012 — record 21072568 — DOI 10.5281/zenodo.21072568 (90 files) shard 0013 — record 21072593 — DOI 10.5281/zenodo.21072593 (90 files) shard 0014 — record 21072638 — DOI 10.5281/zenodo.21072638 (90 files) shard 0015 — record 21072672 — DOI 10.5281/zenodo.21072672 (90 files) shard 0016 — record 21072738 — DOI 10.5281/zenodo.21072738 (90 files) shard 0017 — record 21072771 — DOI 10.5281/zenodo.21072771 (90 files) shard 0018 — record 21072839 — DOI 10.5281/zenodo.21072839 (90 files) shard 0019 — record 21072877 — DOI 10.5281/zenodo.21072877 (90 files) … and 171 more — see the README (in this record's files) for the full list.