Protocol full text hidden due to copyright restrictions
Open the protocol to access the free full text link
AMP prediction: users can (i) predict AMPs (ii) predict antimicrobial region within peptides and (iii) rationally design AMPs by generating an exhaustive combinatorial library of sequences for a user-defined sequence and predict effect of single residue substitutions on antimicrobial activity using SVMs, RF and DA.
BLAST: users can use BLAST tool (26 (link)) to query protein sequence/s against various data sets of CAMPR3 which include the entire database, sequence, structure, patent, experimentally validated, predicted and predicted based on signature data sets to find homologous sequences, structures and other relevant information.
Clustal Omega: users can use Clustal Omega tool of EMBL-EBI to obtain multiple sequence alignment of peptides.
Vector Alignment Search Tool: users can identify similar protein structures and distant homologs that cannot be identified by sequence comparison using VAST of NCBI (27 (link)).
PRATT: users can generate AMP family-specific patterns using this tool from ExPASy.
ScanProsite: using this tool from Swiss Institute of Bioinformatics, users can (i) scan proteins against the PROSITE collection of PSSMs/patterns; (ii) scan patterns against protein sequence, structure or user defined database/s and (iii) scan user defined patterns against a set of protein sequences.
PHI-BLAST: users can use PHI-BLAST (28 (link)) to find AMPs similar to the query based on a family-specific pattern.
jackhmmer: users can iteratively search a protein sequence/structure database using a set of protein sequences/multiple sequence alignment/HMM as an input to find homologs using this tool from EMBL-EBI.
Protocol full text hidden due to copyright restrictions
Open the protocol to access the free full text link