Characterization of Inner Cavity Lining of Proteins
What does CICLOP do?
CICLOP is a tool for detection and characterization of tunnels/channels/pores or inner cavities that are part of proteins. Tunnels or channels are paths that connect an internal point with the exterior of the protein. A pore is a type of channel that traverses the entire protein (from one point on the surface to another). Inner cavities are deep clefts on the inside of protein that are usually water inaccessible.
Can I submit more than one PDB file?
Yes, CICLOP allows for the submission of more than one PDB. While uploading the file, you can simply select as many files as you wish, however, the results of each submission are sent separately. Please note that the parameters for all the structures submitted are taken to be the same as those at the time of submission. This includes the calculation of conservation scores as well as the FASTA file submitted (if any). To prevent erroneous results, the users are encouraged to submit PDBs with a FASTA sequence separately and not together as a batch.
Which mode of alignment should I use for my protein? Automatic or Manual?
Most proteins work well with automatic mode of alignment, however, if your protein does not yield good results with automatic mode, you may try manually aligning the protein’s pore along the Z-axis as shown here.
What should I do if CICLOP detects the incorrect cavity in the automatic mode?
CICLOP offers a manual mode of alignment where you can align your cavity along the Z -axis manually and submit the new structure as an input. For more details on how to manually align cavities, please refer here.
How can I visualize the cavity in my protein?
CICLOP provides a cavity.pqr file as one of its outputs. This file can be loaded into any molecular visualization software (for example UCSF Chimera and be rendendered as spheres). This image is a representation of the volume enclosed within the protein cavity(s) detected by CICLOP.
I can not understand the residue.dat file in the CICLOP output.
This file lists out all the residues that were detected to be lining the protein inner cavity(s). Each entry is separated by a comma and consists of the residue number (preceding the dot) as well as its corresponding chain ID (after the dot) from the PDB file.
How can I visualize the residues lining my protein’s cavity?
CICLOP provides an inner_surface_marked.pdb file which is a B factor loaded output file. It can be loaded in any molecular visualization software and rendered to highlight residues that line the cavity. For details about cavity and residue visualization, please refer here.
What do the Charge distribution and Hydrophobicity plots mean?
CICLOP characterizes the cavity in terms of its physicochemical properties by generating the charge distribution as well as hydrophobicity profile along the pore axis. The charge distribution is a simple addition of the total number of positively as well as negatively charged residues along the pore axis amongst the total residues detected to line the inner cavity. Similarly, the hydrophobicity plot is computed by adding the hydrophobicities of each residue detected on the inside surface, according to the Kyte and Doolittle hydrophobicity scale.
Should I submit a FASTA file for calculating the conservation scores of the protein cavity?
In case a FASTA file is not submitted, CICLOP generates the protein sequence using the input PDB. This might give erroneous results in cases where the input structure contains missing regions. Therefore, in such scenarios, the user is advised to provide a FASTA file in case they wish to generate the conservation profile of the cavity. Please ensure that the FASTA file provided as the input conforms to the format shown here.
What does a conservation profile mean?
The conservation profile is generated according to the evolutionary scores calculated based on multiple sequence alignment of the reference sequence (obtained either through the FASTA file or from the input PDB) with other similar sequences (obtained using PSI-BLAST or jackhmmer). After successfully mapping the evolutionary scores calculated onto the inner lying residues, CICLOP moves through the structure along the pore axis. The residues lying on the inner surface in each step are then divided into one of the 5 following groups based on the conservation score assigned to them: (Highly Conserved(1-2), Moderately Conserved(3-4), Neutral(5), Moderately Unconserved(6-7), Highly Unconserved(8-9)). This is represented as a color coded plot with the number of residues on the X axis and the distance along the cavity on the Y axis.
Can I download CICLOP on my local machine?
Yes, CICLOP is available as a standalone for linux and can be downloaded from the Downloads section on the web server.
I still have some doubts about the tool, how can I contact the authors?
We would be more than happy to hear from you. You can mail us at parth18401@iiitd.ac.in with your queries or suggestions. Or you can simply fill the form provided at the bottom of the Home page.