PROFBVAL(1)

📦
version 1.0.22 · 2 versions
, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble

💖 PROFBVAL — the profbval(1) glow-up 💖

okay bestie, gather round, because this one is a user command and it's lowkey iconic. it lives in the manual, it predicts stuff, and it's about to be your new fave. let's go 🦋

✨ NAME ✨

profbval — predicts flexible/rigid residues straight from the sequence. no cap. 💅

✨ SYNOPSIS ✨

like, here's how you actually call her:

profbval <FASTA_FILE> <RDBPROF_FILE> <HSSP_FILE>
<OUTPUT_FILE[,OUTPUT_FILE,...]> <WINDOW> <OUTPUT_MODE[,OUTPUT_MODE,...]>
<DEBUG>

✨ DESCRIPTION ✨

so PROFbval is a neural network that was trained on backbone B-value data from X-ray structures. fr fr. she was trained on a sequence-unique set of high-resolution protein structures from the PDB. 👑

here's the tea: the mobility of a given residue on the protein surface is related to its functional role. and a super common way to measure atom mobility in proteins is B-value data from x-ray crystallography structures. PROFbval is a method that predicts backbone B-values from amino-acid sequence. she's useful for both protein structure and function predictions — like, a biologist can locate potentially antigenic determinants by identifying the most flexible residues on the protein surface 🌸, and a crystallographer can locate residues that potentially have high experimental B-values. two for one, ate. ✨

🧬 Conversion of PSI-BLAST alignment to HSSP format

the most up-to-date procedure lives at:

https://www.rostlab.org/owiki/index.php/How_to_generate_an_HSSP_file_from_alignment#Generating_an_HSSP_profile

and here are the steps, bestie, in order:

  1. Convert BLAST output to a Single Alignment Format (SAF):
/usr/share/librg-utils-perl/blast2saf.pl fasta=<query_fasta_file> maxAli=3000 eSaf=1 \
 saf=<saf_formatted_file> <blast_output>
  1. Convert SAF format to HSSP:
/usr/share/librg-utils-perl/copf.pl <saf_formatted_file> formatIn=saf formatOut=hssp \
 fileOut=<hssp_formatted_file> exeConvertSeq=convert_seq
  1. Filter results to 80% redundancy:
/usr/share/librg-utils-perl/hssp_filter.pl red=80 <hssp_formatted_file> fileOut=<filtered_hssp_formatted_file>

📊 Output format

this description applies to the default output format, mwah 💋

  • number — residue number
  • residue — residue type
  • raw — raw value of the different between the two output nodes
  • Bnorm — predicted normalized B-value. the values are normalized so that in a given sequence the average value is 0 and the standard deviation is 1. the higher the value, the more flexible a residue is predicted to be. 📈
  • Non-strict mode (NS) — indicates on a flexible residue. according to the NS mode most of the residues are flexible; hence, a residue on the surface that is predicted to be rigid is likely to have a functional role. 🤔
  • Strict mode (S) — indicates on a flexible residue. according to the S mode about a third of the residues are flexible, therefore, a stretch of residues that is predicted to be flexible might be important for the protein function. 🔥

✨ REFERENCES ✨

  • Schlessinger A, Yachdav G, & Rost B. PROFbval: predict flexible and rigid residues in proteins. Bioinformatics. 2006 Apr 1;22(7):891-3.
  • Schlessinger A, Rost B. Protein flexibility and rigidity predicted from sequence. Proteins. 2005 Oct 1;61(1):115-26.

the receipts, periodt. 📚

✨ OPTIONS ✨

here's where it gets juicy. every single one, no skips:

  • FASTA_FILE — file containing protein amino-acid sequence in fasta format.
  • RDBPROF_FILE — secondary structure and solvent accessibility prediction by PROF in rdb format.
  • HSSP_FILE — PSI-BLAST alignment profile file converted to HSSP format.
  • OUTPUT_FILE — the name of the final PROFbavl output file. you may give multiple output files. you then probably want to give a list of output modes as well, one for each output file. separate entries with , (comma is not allowed in the file name). 🙈
  • WINDOW — this is the desired smoothing window for the output. the method was trained on window of 9.
  • OUTPUT_MODE — PROFbval can create output files in different formats for different purposes. the default output mode for the package is 6. you may give multiple output modes. you then probably want to give a list of output files as well, one for each output mode. separate entries with ,.
    • Modes: '-1', '0', '1', '2', '3', '4', '5', '6', 'snap', 'snapfun'
    • 5 — for metadisorder(1)
    • snap, snapfun — for snapfun(1)
  • DEBUG — Default: 0. Enable with 1.

✨ EXAMPLE ✨

copy-paste era, go off:

profbval /usr/share/doc/profbval/examples/cad23.f /usr/share/doc/profbval/examples/cad23-fil.rdbProf /usr/share/doc/profbval/examples/cad23-fil.hssp cad23.profbval 9 6

✨ ENVIRONMENT ✨

  • PROFBVAL_ROOT — the directory used to look up ./scr/createDataFile.pl, ./scr/PROFbval.pl and ./nn_files/jct.in. if unset, /usr/share/profbval is used. 💜

✨ FILES ✨

  • *.profbval — default output file extension
  • /usr/share/doc/profbval/examples — default precomputed input files directory

✨ NOTES ✨

  1. it is recommended to create the profiles using 3 iteration of PSI-BLAST against big database
  2. it is also recommended to filter the hssp files using hssp_filter.pl from the Prof package using the following command: perl hssp_filter.pl hssp_file red=80
bestie, these are recommendations, not vibes-based suggestions. do them. 🫶

✨ AUTHOR ✨

A. Schlessinger <avnersch@gmail.com>

✨ SEE ALSO ✨

and that's the whole page, no crumbs left. 🌈

this was version 1.0.22, dated 2022-01-18 — so yeah, she's been serving since way back. stan a classic. 💖✨🎀

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