Гомологичное моделирование комплекса белка с лигандом.

• Полученное с помощью ClustalW выравнивание лизоцима форели с моим белком:
  align.pir

• Обработанный файл структуры лизоцима форели:
  1lmp_now.ent

• Контакты из исходной молекулы

  /all//A/SER`32/NE1 - /ligand//A/NAG`138/O6C y
  /all//A/GLN`34/N - /ligand//A/NAG`138/O6C  y
  /all//A/ASN`46/NE1 - /ligand//A/NAG`138/O1L y
  
  

  
  
  Новые контакты:

  /all//A/THR`36/ND2 - /ligand//A/NDG`138/O6C 
  /all//A/GLN`39/N - /ligand//A/NAG`138/O6C  
  /all//A/ASN`50/NE1 - /ligand//A/NAG`138/O1L 
   
  
  

• Скрипт на вход Modeller: lys_bpt5.py

• Оценка качества модели.
  bpt5.B99990001.pdb
  bpt5.B99990002.pdb
  bpt5.B99990003.pdb
  bpt5.B99990004.pdb
  bpt5.B99990005.pdb
  

  № - Ramachandran plot evaluation - Standard deviation of omega values
  1 - (-2.024) - 5.514
  2 - (-2.297) - 5.655
  3 - (-1.330) - 5.217
  4 - (-1.759) - 5.124
  5 - (-1.766) - 6.710
  i - (-0.977) - 2.708
  
  The Ramachandran plot is probably the very best indicator of the quality of the 
  experimental determination of three dimesional protein coordinates. 
  This server analyses the Ramachandran plot of a PDB file and compares it with the 
  Ramachandran plots of about 400 representative structures solved at high resolution. 
  The score expressing how well the backbone conformations of all residues
  correspond to the known allowed areas in the Ramachandran plot is a bit low.
  
  The omega angles for trans-peptide bonds in a structure is expected to give a
  gaussian distribution with the average around +178 degrees, and a standard
  deviation around 5.5. In the current structure the standard deviation agrees
  with this expectation.
  

  
  
  Исходя из полученных оценок, выбираем 3 модель.