amaurypm Goto Github PK
Name: Amaury Pupo
Type: User
Bio: I am a Biochemist, with a PhD in Neuroscience and with a strong background in Computational Biology and Bioinformatics.
Amaury Pupo's Projects
assess_dope
Assess models previously generated with modeller with the DOPE method
cmpimg
Compare a set of images and report a structural similarity index (ssim) matrix, in CSV and Mega-compatible formats.
cubediff
Substract two electrostatic maps, contained in Gaussian cube files, and generate a new electrostatic map with the difference.
cubedist
Calculate the pairwise distances (euclidean and rmsd) between a set of electrostatic maps, contained in Gaussian cube files, and report these distances in CVS and a Mega compatible formats.
extract_fragment
Extract rosetta commons fragments from PDB
getchain
Take a selection of chains from a set of structures and save them as new structures.
noxseq
Given a set of protein sequences filters out these with non-standard residues. If not input file given it reads from the standard input and if not output file given it writes to standard output.
pseqsid
Calculates pairwise sequence identity, similarity and normalized similarity score of proteins in a multiple sequence alignment.
pyrmsdmat
Superimpose a set of protein structures and report a RSMD matrix, in CSV and Mega-compatible formats, using Pymol as a module
reducepdf
Reduce PDF file size without noticeable quality loss.
rmsdmat
Superimpose a set of protein structures and report a RSMD matrix, in CSV and Mega-compatible formats.
scrambleseq
Scramble peptide sequences in FASTA format.
seqstats
Print basic stats from sequence files.
splitseq
Split fasta or other sequences files into individual sequences.
struct2seq
Extract chains' and polypeptides' sequences from PDB or mmCIF files.
transcode2h264
Unattended video transcoder to H264 and ACC codecs, in MKV containers.
transcode2h265
Unattended video transcoder to H265 and ACC codecs, in MKV containers.
transcode2xvid
Unattended video transcoder to XVID and MP3 codecs, in AVI containers.
uniqseq
Remove duplicated protein/nucleic acid sequences, keeping the first occurrence.
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