SERAPhiC: A benchmark for in silico fragment-based drug design

Angelo D. Favia*, Giovanni Bottegoni, Irene Nobeli, Paola Bisignano, Andrea Cavalli

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

16 Citations (Scopus)


Our main objective was to compile a data set of high-quality protein-fragment complexes and make it publicly available. Once assembled, the data set was challenged using docking procedures to address the following questions: (i) Can molecular docking correctly reproduce the experimentally solved structures? (ii) How thorough must the sampling be to replicate the experimental data? (iii) Can commonly used scoring functions discriminate between the native pose and other energy minima? The data set, named SERAPhiC (Selected Fragment Protein Complexes), is publicly available in a ready-to-dock format ( It offers computational medicinal chemists a reliable test set for both in silico protocol assessment and software development.

Original languageEnglish
Pages (from-to)2882-2896
Number of pages15
JournalJournal of Chemical Information and Modeling
Issue number11
Publication statusPublished - 28 Nov 2011
Externally publishedYes

ASJC Scopus subject areas

  • General Chemistry
  • General Chemical Engineering
  • Computer Science Applications
  • Library and Information Sciences


Dive into the research topics of 'SERAPhiC: A benchmark for in silico fragment-based drug design'. Together they form a unique fingerprint.

Cite this