ProtSweep/ 2Dsweep / DomainSweep
Protsweep can be used for analysis and possible identification of newly obtained protein sequences.
2DSweep is a task for performing secondary structure predictions on protein sequences.
DomainSweep identifies the domain architecture within a protein sequence and thus can help find correct functional assignments for an uncharacterised protein sequence.
HUSAR Bioinformatics Lab
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Nucleic Acids Res. 2007 Jul;35(Web Server issue):W444-50. Epub 2007 May 25.
ProtSweep, 2Dsweep and DomainSweep: protein analysis suite at DKFZ.
del Val C1, Ernst P, Falkenhahn M, Fladerer C, Glatting KH, Suhai S, Hotz-Wagenblatt A.
CAVER 3.02 / CAVER Analyst 1.0
CAVER is a software tool for analysis and visualization of tunnels and channels in protein structures. Tunnels are void pathways leading from a cavity buried in a protein core to the surrounding solvent. Unlike tunnels, channels lead through the protein structure and their both endings are opened to the surrounding solvent. Studying of these pathways is highly important for drug design and molecular enzymology.
CAVER can be used either as PyMol plugin or independent application CAVER Analyst.
Protein Engineering Group, Loschmidt Laboratories
CAVER / CAVER Analyst
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Bioinformatics. 2014 May 29. pii: btu364. [Epub ahead of print]
CAVER Analyst 1.0: Graphic tool for interactive visualization and analysis of tunnels and channels in protein structures.
Kozlikova B, Sebestova E, Sustr V, Brezovsky J, Strnad O, Daniel L, Bednar D, Pavelka A, Manak M, Bezdeka M, Benes P, Kotry M, Gora A, Damborsky J, Sochor J.
CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures.
Chovancova E, Pavelka A, Benes P, Strnad O, Brezovsky J, Kozlikova B, Gora A, Sustr V, Klvana M, Medek P, Biedermannova L, Sochor J, Damborsky J.
PLoS Comput Biol. 2012;8(10):e1002708. doi: 10.1371/journal.pcbi.1002708.