What If server
http://swift.cmbi.ru.nl/servers/html/index.html
Molekula pro analýzu – pdb kód 1PW2
What If server
Administration
● List a residue – informace o vybraném residuu
● List a file – základní informace o residuích v
souboru
● List sequence of PDB file – sekvence AK z PDB
souboru – z hlavičky souboru
● Make sequence from PDB file – sekvence AK
vytvořená z PDB souboru
● Renumber a PBD file from 1 – přečíslování residuí
v souboru od 1
Build, check, repair model
● Homology modelling
● Template structure check
● Protein structure check
● Complete a structure
● Remove bumps from structure
● Compare a model to a solvated structure
● Prepare pdb file for docking programs
● Prepare files for Gromacs MD run
Build, check, repair model
Build, check, repair model
Build, check, repair model
Structure validation
● Name check
● Coarse packing quality control
● Anomalous bond lengths
● Planarity
● Fine packing quality control
● Collisions with symmetry axes
● Hand check
● Omega
● Proline puckering
Structure validation
Structure validation
Structure validation
Structure validation
Structure validation
Structure validation
Analyse a residue
● Residue accessibility
● List a residue
● Distance dependent contact of one residue with
polar residues
Protein analysis
● Secondary structure, symmetry and accessibility
● Torsion angles
● Accessible polar fraction
● Check for short interatomic distances (bumps)
● Relative surface exposure
● Analyse protein-cofactor contacts
● Analyse protein-DNA/RNA contacts
● Bond angles
Protein analysis
Protein analysis
Protein analysis
Protein analysis
Protein analysis
Protein analysis
3-D graphics
3-D graphics – arrows and cylinders
3-D graphics – backbone with H-bonds
3-D graphics – B-factor coloring
Ramachandran plot
2-D graphics – Ramachandran plot
Hydrogen (bonds)
Hydrogen (bonds)
Hydrogen (bonds)
Hydrogen (bonds)
Accessibility
Accessibility
Accessibility
Atomic contacts
Atomic contacts
Coordinate manipulation
Crystal symmetry
Crystal symmetry
Other options
Residue contacts
Úkoly:
● Vykreslete Ramachandranův diagram pro molekulu
s PDB kódem 3S2P
● Zjistěte kontakty residui této molekuly s ligandem
● Vypište sekvenci AK v proteinu
● Vytvořte graf kontaktů mezi residui v proteinu