PROFISIS(1)

💖 PROFISIS(1) — User Commands 💖

okay bestie, listen up, we're doing profisis today, it's from the User Commands corner of the manual and honestly? it's giving ✨ computational biology icon ✨. sit down, grab a strawberry 🍓, and let's get into it.

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🌸 NAME 🌸

profisis — protein-protein interaction sites identified from sequence

like, that's the whole vibe. it finds where proteins touch each other, and it does it from sequence alone. no cap. 🦋

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🎀 SYNOPSIS 🎀

profisis [OPTION]

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✨ DESCRIPTION ✨

so profisis (also known as ISIS) is a machine learning-based method that identifies interacting residues from sequence alone. and when I say alone I mean ALONE — the method was developed using transient protein-protein interfaces from complexes of experimentally known 3D structures, but it never explicitly uses 3D information. nope. not once. 🙈

instead, we combine predicted structural features with evolutionary information. the way that works is genuinely so clever.

the strongest predictions of the method reached over 90% accuracy in a cross-validation experiment. NINETY. PERCENT. 🔥

and the results suggest something kind of beautiful: despite the significant diversity in the nature of protein-protein interactions, they all share common basic principles — and those principles are identifiable from sequence alone. it's giving "we're all connected" main character energy, fr fr 💜

🧬 Conversion of PSI-BLAST alignment to HSSP format 🧬

the most up-to-date procedure can be found at https://www.rostlab.org/owiki/index.php/How_to_generate_an_HSSP_file_from_alignment#Generating_an_HSSP_profile

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>

2. 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

3. 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 📄

see description of --outformat option. (spoiler: it's down there in OPTIONS, keep scrolling bestie 🫶)

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📚 REFERENCES 📚

Ofran, Y. and Rost, B. (2007). ISIS: interaction sites identified from sequence. Bioinformatics, 23(2), e13-6.

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💅 OPTIONS 💅

🫶 Required parameters

• --fastafile — file that contains your sequence in fasta format. mandatory. non-negotiable. the assignment is due. 📌
• --hsspfile — file with hssp data for sequence in --fastafile. they're a matching set, like you and your bestie.
• --rdbproffile — file with prof output for sequence in --fastafile. yes, again for the same sequence. it takes a village.
• --outfile — output file. this is where the magic lands. ✨

🌈 Optional parameters

• --outformat — output format [pp|prval], default=pp
  • pp — PredictProtein format:

Output ::= Header_Line Binary_Out Raw_Out

Header_Line ::= '>' Header_String '\n'

Binary_Out ::= ( Horiz_Sequence '\n' Bin_Pred '\n\n' )+

Horiz_Sequence ::= Amino_Acid_One_Letter_Code{,40}

Bin_Pred ::= [P-]{,40}

P marks binding residue. that's the tea right there 👑

Raw_Out ::= ( Amino_Acid_Number ' ' Amino_Acid_One_Letter_Code ' ' Prediction_Score '\n' )+

Prediction_Score ::= Integer_Value

see example outputs in /usr/share/doc/profisis/examples.

• prval — ( 'resn resi predicted_value' )+, e.g.

'1 M 25'
'2 R 36'
...

• --debug
• --nodebug — default: --nodebug
• --succinct — succinct output (print no confidence values). keeping it short and mysterious, love that for us 💀

🧚 Parameters controlling post processing — these parameters affect only the top part of the pp output format

• --gap=int — default=20
• --stretch=int — default=5
• --crd=int — default=7
• --crd-restriction
• --nocrd-restriction — default: --crd-restriction. use original ($crd = undef) code (--crd-restriction) or use new ($cr) code (--nocrd-restriction).

okay so that last one is literally a choice between the old code path and the new code path, and the default is the original one. no editorialising from me, that's just what it says 🌸

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🌟 EXAMPLES 🌟

profisis --fastafile /usr/share/doc/profisis/examples/3A1P_A.fasta --hsspfile /usr/share/doc/profisis/examples/3A1P_A.hssp --rdbproffile /usr/share/doc/profisis/examples/3A1P_A.rdbProf --outfile /tmp/3A1P_A.profisis

look at that. a whole pipeline in one line. ate. 🔥

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🌱 ENVIRONMENT 🌱

• PROFISISCONF — location of configuration file to use, overriding other configuration files

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📂 FILES 📂

• /usr/share/profisis/profisisrc.default — default configuration file. see this file for a description of the parameters.
• /etc/profisisrc — system configuration file overriding values in /usr/share/profisis/profisisrc.default
• ~/.profisisrc — user configuration file overriding values in /etc/profisisrc
• $PROFISISCONF — if this environment variable is set ~/.profisisrc is disregarded and the value of the variable is read for configuration options overriding /etc/profisisrc

so the config stack goes default → system → user → and then $PROFISISCONF just straight up disregards your user file. it said "not today" 💀

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👑 AUTHOR 👑

Yanay Ofran and Burkhard Rost

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🔗 SEE ALSO 🔗

prof(1)

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and that's the whole page bestie, you're officially fluent in profisis 💜

version 1.0.11, dated 2022-01-18, from the PROFISIS(1) manual — mwah, go identify some interaction sites, you got this 🎀✨🦋