Difference between revisions of "Lab journal task 4"

From Bioinformatikpedia
Line 39: Line 39:
   
 
LGA: <br>
 
LGA: <br>
* superimpose to target structure (second structure, inour case 1A6Z )
+
* superimpose to target structure (second structure, in our case 1A6Z )
 
* default parameters
 
* default parameters
 
SSAP: <br>
 
SSAP: <br>
Line 45: Line 45:
 
* no parameters to set
 
* no parameters to set
 
*score from 0 to 100
 
*score from 0 to 100
  +
TopMatch: <br>
  +
* target 1A6Z
  +
* default parameters
  +
* target in blue, query in green
  +
* structurally equivalent residue pairs: orange (query) and red (target)
  +
* S = Measure of structural similarity based on Gaussian functions (see Sippl & Wiederstein (2012)). If the structurally equivalent parts in query and target match perfectly, S is equal to L. With increasing spatial deviation of the aligned residues, S approaches 0.
  +
* S_r = Typical distance error. For details on the construction of this per-residue measure of structural similarity, see Sippl & Wiederstein (2012).
  +
Er
  +
   
 
number of alignet residues per pair
 
number of alignet residues per pair

Revision as of 22:57, 10 August 2013

<css> table.colBasic2 { margin-left: auto; margin-right: auto; border: 2px solid black; border-collapse:collapse; width: 70%; }

.colBasic2 th,td { padding: 3px; border: 2px solid black; }

.colBasic2 td { text-align:left; }

.colBasic2 tr th { background-color:#efefef; color: black;} .colBasic2 tr:first-child th { background-color:#adceff; color:black;}

</css>


The following four alignment methods were used:

LGA:
  • superimpose to target structure (second structure, in our case 1A6Z )
  • default parameters
SSAP:
  • no target structure to specify
  • no parameters to set
  • score from 0 to 100
TopMatch:
  • target 1A6Z
  • default parameters
  • target in blue, query in green
  • structurally equivalent residue pairs: orange (query) and red (target)
  • S = Measure of structural similarity based on Gaussian functions (see Sippl & Wiederstein (2012)). If the structurally equivalent parts in query and target match perfectly, S is equal to L. With increasing spatial deviation of the aligned residues, S approaches 0.
  • S_r = Typical distance error. For details on the construction of this per-residue measure of structural similarity, see Sippl & Wiederstein (2012).
Er number of alignet residues per pair 1DE4_A 1QVO_A 1S7X_A 1JFM_A 2IA1_A 3NCI_A 1VZY_A 1MUS_A
method name location
LGA http://proteinmodel.org/AS2TS/LGA/lga.html
SSAP http://protein.hbu.cn/cath/cathwww.biochem.ucl.ac.uk/cgi-bin/cath/GetSsapRasmol.html
TopMatch https://topmatch.services.came.sbg.ac.at/
CE http://source.rcsb.org/jfatcatserver/index.jsp