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Fig. 6 | Journal of Cheminformatics

Fig. 6

From: bSiteFinder, an improved protein-binding sites prediction server based on structural alignment: more accurate and less time-consuming

Fig. 6

a Unbound chain (PDB ID: 1bbs, CHAIN ID: A, blue) and related appropriate template (PDB ID: 1hrn, CHAIN ID: B, yellow). After mapping the ligand (03D, red) in template to unbound chain, a new stable bound structure is formed with the tightly binding between the ligand and unbound chain. The top 20 templates at most ranked according to the similarity would be subsequently clustered. b Unbound chain (PDB ID: 1bbs, CHAIN ID: A, blue) and related appropriate template (PDB ID: 3g6z, CHAIN ID: A, yellow). After mapping the ligand (NAG, red) in template to unbound chain, a new stable bound structure could not be formed. The reason is that there are more residues (see the red circle) in template than unbound chain which have a close connection with the ligand

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