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. Author manuscript; available in PMC: 2011 May 21.
Published in final edited form as: Biopolymers. 2010 Nov;93(11):936–951. doi: 10.1002/bip.21474

FIGURE 3.

FIGURE 3

Coarse-grained representations of GG and GG-PTX residues. Mapping of the AA models to CG models was done according to the MARTINI force field. Roughly 4–5 heavy atoms were assigned to one interaction center, or “bead”. (For the aromatic groups in Paclitaxel, the assignment was 2 heavy atoms to 1 bead.) GG was reduced from 18 or 19 heavy atoms to 4 beads, and GG-PTX was reduced from 148 heavy atoms to 27 CG beads. Differently colored beads represent different bead types, based on polarity and hydrogen-bonding capabilities. For each bead, four main types are considered: polar (P), nonpolar (N), apolar (C), and charged (Q). Each main type can subsequently be distinguished by its degree of polarity (from 1 = lowest polarity to = 5 highest polarity) and its hydrogen-bonding abilities (denoted by a letter: donor (d), acceptor (a), both (da), or none (0)). Beads with nomenclature beginning ‘B’ and ‘S’ letters denote a backbone bead and an aromatic bead, respectively.