1 {% extends "base.html" %}
3 {% load i18n lazysignup_tags %}
7 Input data description:</h4>
11 As input Unres server can use protein sequence given using one letter code
12 (with XX to mark a new chain) or PDB files.
14 Only standard codes of aminoacids are recognized in PDB files.
16 Unres server requires input PDB files with continuous (without breaks)
17 protein chains. PDB files with gaps in the structure have to be first prepared
18 by filling up all missing residues. There is a plan to add such service to
19 the UNRES server but currently, a user has to model missing fragment using
20 external software or online servers (for example Modeller software, Modloop
23 Disulfide bonds are read from PDB based on SSBOND records and for multichain
24 protein COMPND record with propers CHAIN: tokens listing all chains in the
25 PDB file. See example:
27 COMPND 3 CHAIN: A, B, C, D;
28 SSBOND 1 CYS C 107 CYS C 138
29 SSBOND 2 CYS C 124 CYS C 139
30 SSBOND 3 CYS C 137 CYS C 149
31 SSBOND 4 CYS D 107 CYS D 138
32 SSBOND 5 CYS D 124 CYS D 139
33 SSBOND 6 CYS D 137 CYS D 149
35 <li> A protein structure with disulfide bonds and no corresponding
36 SSBOND records will result in clashes and a very high energy
37 which can crash calculations.
39 TER records in PDB file are read to recognize chain's ends.
41 Distance distribution (from SAXS experiment) can be added for MREMD
42 simulation in advanced mode. First column distance in Angstroms, second column
43 distribution function value (separated by space).