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Table 1 Conformation sampling methods

From: BCL::Conf: small molecule conformational sampling using a knowledge based rotamer library

Method Search space Search strategy Search method Scoring function
Caesar [ 39] Incremental search of torsion angles combined with distance geometry for ring systems Fragment based Systematic CHARMm force field
Catalyst [ 40] Incremental search of torsion angles with subsequent energy minimization Non-fragment based Simulation (MD) CHARMm force field
Conan [ 41] Incremental search of torsion angles Fragment based Systematic
Confab [42] Incremental search of torsion angles Non-fragment based Systematic MMFF94
Confgen [ 31] Random walk on energy surface calculated using a truncated version of OPLS_2001 Non-fragment based Simulation (MC) MMFFs/OPLs_2001
Corina [ 43] Knowledge based rules derived from CSD Non-fragment based Systematic Reduced force field for optimizing only ring systems
Enumerated Torsions (et) [18] Incremental search of rule-based torsion angles Non-fragment based Systematic
Mimumba [ 15] Incremental search of knowledge-based torsion angles from CSD Non-fragment based Systematic Relative frequency of experimentally observed conformations
Moe (low mode MD) [44] Constant temperature MD Non-fragment based Simulation (MD) MMFF94
Moe (stochastic search) [22] Random perturbations of rotatable bonds in increments biased around 30° Non-fragment based Simulation (MC) MMFF94
Moe (Confimport) [22] Pregenerated fragment conformations obtained from stochastic-search Fragment-based Simulation MMFF94
Moe (systematic) [32] Incremental search of torsion angles Non-fragment based Systematic MMFF94
Omega [ 33] Knowledge based torsions from analysis of molecules in PDB and conformations generated by MMFF94 Fragment based Systematic MMFF94
RDKit [ 34] Distance geometry Non-fragment based Simulation (distance geometry) UFF