. Author manuscript; available in PMC: 2018 Feb 1.

Published in final edited form as: Nat Protoc. 2017 Jan 12;12(2):255–278. doi: 10.1038/nprot.2016.169

TABLE 2.

Important classes of direct docking algorithms

Method class	Properties		Examples
Method class	Search Method	Protein Flexibility	Examples
Global systematic rigid body docking	Fast Fourier Transform; Geometric matching	Minimal; smooth potential allows for some overlaps	ZDOCK⁵³, GRAMM⁷⁸, PIPER¹⁶, DOCK/PIERR¹²⁰
Medium-range methods: Localized searches over selected regions	Monte Carlo minimization; Multi-start quasi-Newton minimizer with side chain search	Moderate, mostly side chains, some loops; motion along normal modes	RosettaDock⁶⁷ ICM-DISCO¹²¹ ATTRACT⁶⁸ SWARMDOCK⁷⁴
Restraint-based docking	Supported by a priori information in the scoring function	Can be more substantial if restraints are available	HADDOCK⁶⁹