help_text='coupling to the thermal bath (Berendsen)')
md_scal_fric = forms.FloatField(label='scal_froc',initial=0.02,
help_text='scaling of the friction coefficients (Langevin)')
+ md_respa = forms.BooleanField(required=False,initial=True,label='RESPA')
md_mdpdb = forms.BooleanField(required=False,label='trajectory as PDB')
boxx = forms.FloatField(label='Box X',initial=1000.0,
# remd_traj1file = forms.BooleanField(required=False,label='single trajectory file',initial='true')
# remd_rest1file = forms.BooleanField(required=False,label='single restart file',initial='true')
+ md_respa = forms.BooleanField(required=False,initial=True,label='RESPA')
+
boxx = forms.FloatField(label='Box X',initial=1000.0,
help_text='box x dimension')
boxy = forms.FloatField(label='Box Y',initial=1000.0,
if seq[-1]=='X':
dimen3-=1
- nogly ='CDSQKIPTFNHLRWAVEYM'
+ nogly ='CDSQKIPTFNHLRWAVEYMcdsqkiptfnhlrwaveym'
seq2 = ''.join([c for c in seq if c in nogly])
dimen3=(dimen3+len(seq2))*3
</li>
<li>
+A. Liwo, S. Ołdziej, C. Czaplewski, D. Kleinerman, P. Blood and H.A.
+Scheraga. Implementation of molecular dynamics and its extensions with the
+coarse-grained UNRES force field on massively parallel systems; towards
+millisecond-scale simulations of protein structure, dynamics, and
+thermodynamics. <i>J. Chem. Theory Comput.<i> 2010, 6, 890-909.
+</li>
+
+<li>
A. Liwo, M. Baranowski, C. Czaplewski, E. Gołaś, Y. He, D. Jagieła,
P. Krupa, M. Maciejczyk, M. Makowski, M.A. Mozolewska, A. Niadzvedtski,
S. Ołdziej, H.A. Scheraga, A.K. Sieradzan, R. Ślusarz, T. Wirecki, Y. Yin,
<i>J. Chem. Inf. Model.</i> 2017, 57, 2364–2377.
</li>
+<li>
+A. Karczyńska, M.A. Mozolewska, P. Krupa, A. Giełdoń, A. Liwo, C.
+Czaplewski.Prediction of protein structure with the coarse-grained UNRES
+force field assisted by small X-ray scattering data and knowledge-based
+information.
+<i>Proteins: Struct. Funct. Bioinf.</i> 2017, CASP12 special issue DOI: 10.1002/prot.25421
+</li>
+
</ol>
+<p>
+License terms of UNRES package implemented in the server
+<ul>
+<li>
+ This software is provided free of charge to academic users, subject to
+ the condition that no part of it be sold or used otherwise for
+ commercial purposes, including, but not limited to its incorporation
+ into commercial software packages, without written consent from the
+ authors. For permission contact Prof. H. A. Scheraga, Cornell
+ University.
+<li>
+ This software package is provided on an "as is" basis. We in no way
+ warrant either this software or results it may produce.
+<li>
+ Reports or publications using this software package must
+ contain an acknowledgment to the authors and the NIH Resource
+ in the form commonly used in academic research.
+</ul>
+
+Third party software employed in the server
+<ul>
+<li> <a href="http://pymol.org"> pymol </a>
+<li> convpdb.pl from <a href="http://www.mmtsb.org/">MMTSB Tool Set</a>
+<li> tleap, sander and ambpdb from <a href="ambermd.org">Amber Tools</a>
+<li> <a href="http://cssb.biology.gatech.edu/PULCHRA"> pulchra </a>
+<li> <a href="http://dunbrack.fccc.edu/scwrl4/"> Scwrl4</a>
+<li> <a href="https://zhanglab.ccmb.med.umich.edu/TM-score/">tmscore</a>
+</ul>
</div>
</div>
<div class="col-xs-10"> mdpdb </div>
<div class="col-xs-10">{{ task.md_mdpdb}}</div>
</li>
+ <li class="list-group-item task-item">
+ <div class="col-xs-10"> RESPA </div>
+ <div class="col-xs-10">{{ task.md_respa}}</div>
+ </li>
+
+
{% endif %}
{% if task.type == "remd" %}
</li>
{% endif %}
+
+ <li class="list-group-item task-item">
+ <div class="col-xs-10"> RESPA </div>
+ <div class="col-xs-10">{{ task.md_respa}}</div>
+ </li>
<li class="list-group-item task-item">
<div class="col-xs-10"> temperatures </div>
<li>
Disulfide bonds are read from PDB based on SSBOND records and for multichain
protein COMPND record with propers CHAIN: tokens listing all chains in the
-PDB file.
+PDB file. See example:
+<pre>
+COMPND 3 CHAIN: A, B, C, D;
+SSBOND 1 CYS C 107 CYS C 138
+SSBOND 2 CYS C 124 CYS C 139
+SSBOND 3 CYS C 137 CYS C 149
+SSBOND 4 CYS D 107 CYS D 138
+SSBOND 5 CYS D 124 CYS D 139
+SSBOND 6 CYS D 137 CYS D 149
+</pre>
<li> A protein structure with disulfide bonds and no corresponding
SSBOND records will result in clashes and a very high energy
which can crash calculations.
<li>
TER records in PDB file are read to recognize chain's ends.
+<li>
+Distance distribution (from SAXS experiment) cam be added for MREMD
+simulations in advanced mode. First column distance, second column
+distribution function value (separated by space).
</ol>
{% endblock %}
<p>
Finally cluster analysis is performed to select 5 families of conformations,
and representative model from each family is converted to all-atom
-and refined.
+and refined. PDB files can be downloaded by clicking on the picture.
<p>
<a href="static/remd9.png"><img src="static/remd9.png" width="300px"></a>
and replica exchange simulations of 1E0G starting form extended chain
using new UNRES force field and Berendsen thermostat.
+<hr>
+<h4><li>
+Distance distribution restrained (simulated SAXS data)
+replica exchange molecular dynamics of
+Bacteriocin CbnXY (PDB code:5UJQ) starting from the extended chain.
+<br>
+(Use <i>Load example SAXS data</i> button in advanced mode)
+</h4>
+<div>
+ <fieldset class="majorpoints">
+ <legend class="majorpointslegend"
+ style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
+
+ <div class="hiders" style="display:none" >
+<img src="static/saxs1.png" style="border:2px solid blueviolet">
+<br>
+...
+<br>
+<img src="static/saxs2.png" style="border:2px solid blueviolet">
+<p>
+
+Plots of histograms of UNRES energy for each temperature, and
+energy vs temperature are presented.
+The weighted histogram analysis (WHAM) is applied to compute the
+probabilities of the obtained conformations to occur at particular
+temperatures, plots of heat capacity and average RMSD as a functions
+of temperature are shown. Replica exchanges are analyzed.
+<p>
+<a href="static/saxs3.png"><img src="static/saxs3.png" width="300px"></a>
+<a href="static/sasx4.png"><img src="static/saxs4.png" width="300px"></a>
+<a href="static/saxs5.png"><img src="static/saxs5.png" width="300px"></a>
+<a href="static/saxs6.png"><img src="static/saxs6.png" width="300px"></a>
+<a href="static/saxs7.png"><img src="static/saxs7.png" width="300px"></a>
+<a href="static/saxs8.png"><img src="static/saxs8.png" width="300px"></a>
+<a href="static/saxs9.png"><img src="static/saxs9.png" width="300px"></a>
+<a href="static/saxs10.png"><img src="static/saxs10.png" width="300px"></a>
+<p>
+Finally cluster analysis is performed to select 5 families of conformations,
+and representative model from each family is converted to all-atom
+and refined.
+<p>
+<a href="static/saxs12.png"><img src="static/saxs12.png" width="300px"></a>
+
+<p>
+Additionaly the input reference distance distribution and
+distance distributions for 5 final models are plotted.
+<p>
+<a href="static/saxs11.png"><img src="static/saxs11.png" width="300px"></a>
+
+
+</div>
+</div>
+
+
<script src="/static/jquery.min.js"></script>
<script>
three_to_one = dict(res_codes)
def seq_add_x(sequence):
- if sequence[0] != 'G':
+ if sequence[0] != 'G' and sequence[0] != 'g':
sequence='X'+sequence
- if sequence[-1] != 'G':
+ if sequence[-1] != 'G' and sequence[-1] != 'g':
sequence=sequence+'X'
- set ='CDSQKIPTFNGHLRWAVEYMX'
+ set ='CDSQKIPTFNGHLRWAVEYMXcdsqkiptfnghlrwaveym'
sequence = ''.join([c for c in sequence if c in set])
return(sequence)
task.md_scal_fric=form.cleaned_data["md_scal_fric"]
task.md_mdpdb=form.cleaned_data["md_mdpdb"]
task.unres_ff=form.cleaned_data["unres_ff"]
+ task.md_respa=form.cleaned_data["md_respa"]
task.boxx=form.cleaned_data["boxx"]
task.boxy=form.cleaned_data["boxy"]
task.boxz=form.cleaned_data["boxz"]
task.remd_nstex=form.cleaned_data["remd_nstex"]
task.md_ntwx=form.cleaned_data["md_ntwx"]
task.md_ntwe=form.cleaned_data["md_ntwe"]
+ task.md_respa=form.cleaned_data["md_respa"]
# task.remd_traj1file=form.cleaned_data["remd_traj1file"]
# task.remd_rest1file=form.cleaned_data["remd_rest1file"]
projects / django_unres.git / commitdiff
