modplus, a sequence-structure alignment and protein modelling helper tool
(C)2007-2019 Mindaugas Margelevicius, Institute of Biotechnology, Vilnius University
modplus is a helper tool to model the target protein sequence using template structures and MODELLER (Sali and Blundell, J Mol Biol, 234(3), 779-815, 1993). It resolves inconsistencies that may arise between template sequences and structures. The correspondence between a model and the native target structure is optionally calculated with TM-score (Zhang and Skolnick, Proteins, 57(4), 702-710, 2004).
The input file contains aligned sequences in FASTA:
>targetname [chains]; [optional user information]
G-----VDILR-MDAVAF-------IWKQMGTSCE ...
>templ1name [chains]; [optional user information]
FANYDEHLIFEGMNEPRLVGHANEWWPELTNSDVV ...
>templ2name [chains]; [optional user information]
EMLAIAVETKPHFCCLVPEKRQEVTTEGGLDV--A ...
> ...
...
By default, the first sequence is the target to be modelled. Optionally, other sequences (templates) may be modelled as well (see below). One or more template sequences (two or more sequences in total) can be listed in the file. A target is modelled using all the template structures and alignments listed in the file.
The names templ1name, templ2name, ... (and targetname if
options --all and/or --tm are specified) have to correspond to
the filenames (without extension) of PDB structures. Required PDB
files with extension .ent or .pdb added are looked up in the
directory specified by the option --pdb.
Template chains are extracted from pdb files. There may be several
chain identifiers given by chains (e.g., SCOP domains compiled:
ABC). If no chains are given, the first one is identified and
used automatically.
If option --all is specified, each sequence in the input file is
modelled using the other sequence(s) as template(s).
Option --tm implies a model quality check with TM-Score. The
TM-Score output files will appear in the output directory specified
by the option --dir. An optional filename following the --tm
option specifies the following format for the resulting TM-scores
written in this file:
(TM: <TMScore1> <TMScore2>)
<TMScore1> is a score obtained with respect to the whole
structure, and <TMScore2> is a score obtained along the alignment
extent.
For available options, please type modplus.pl -h
Contact: mindaugas.margelevicius@bti.vu.lt