CHEXVIS: a tool for molecular channel extraction and visualization

BMC Bioinformatics

Table 1 Comparison of features supported in different channel extraction tools

	CHEXVIS	MOLE	CAVER	MOLAXIS	POREWALKER
Computation of channels leading to internal molecular sites	Yes	Yes	Yes	Yes	No
Automatic suggestion of internal sites using CSA	Yes	Yes	Yes	No	No
Channels to multiple internal sites	Yes	Yes	Yes	No	No
Filtering of similar channels	No	Yes	Yes	No	No
Computation of pores	Yes	Yes	No	Limited	Only transmembrane pores
Computation of transmembrane pores	Yes	No	No	Limited	Yes
Multiple transmembrane pores	Yes	No	No	No	No
Ranking of pores	Yes	No	No	No	Not applicable
Computation of physico-chemical properties	Yes	Yes	No	No	No
Interactive visualization of physico-chemical properties	Yes	No	No	No	No
Conservation profile	Yes	No	No	No	No
User Interface	Web-server	Web-server and GUI	GUI	Web-server	Web-server
Interactive visualization of channels	Yes	Yes	Yes	No	No
Good default parameters	Yes	Yes	Yes	Limited	Yes
Computation speed	Reasonable	Fast	Reasonable	Reasonable	Slow
PyMOL export	Yes	Yes	Yes	No	No
PyMOL plugin	No	Yes	Yes	No	No

ISSN: 1471-2105