Protein Interactions and Properties Explorer

• Home
• Submit Job
• Help
• About
• Contact

• Info on...

  • Protein Properties
  • Center of Mass
  • Disulfide Interactions
  • Ionic Interactions
  • Hydrophobic Interactions
  • Hydrogen Bond Interactions
  • Aromatic-Aromatic Interactions
  • Aromatic-Sulfur Interactions
  • Cation-Pi Interactions

PIPE : Protein Interaction and Properties Explorer

Help and Guidelines

Contents:

• 1. Overview
  2. Method
  3. Input
  4. Options
  5. Output
  6. Login to workspace
  

1. OVERVIEW

• Interactions within a protein are essential for stability and function of the protein. There are several weak as well as strong interacting forces that typically govern interactions mediated by a protein. We aim to enumerate all such interactions that occur within a protein. Protein Interaction and Properties Explorer (PIPE) is a server which, given the coordinate set of three dimensional structure of a protein or an assembly, computes various interactions such as disulphide bonds, interactions between hydrophobic residues, ionic interactions, hydrogen bonds, aromatic-aromatic interactions, aromatic-sulphur interactions ,cation-pi interactions and electrostatic interactions within a protein. Along with the interactions PIPE can also calculate Center of mass for a protein with optional addition of hydrogens. It also measures various basic properties of proteins such as atomic composition, amino-acid composition, molecular weight, theoretical isoelectric point, aliphatic index, estimated half-life, extinction coefficient , solubility, Grand Average of Hydropathicity (GRAVY).

  *Interactions and properties are calculated using the standards published in literature.

2. METHOD

• For a given input all possible interacting residue pairs are enumerated along with the interatomic distances and angles. Interactions are identified using standards available in the literature. For details switch to references section.

3. INPUT

• • upload query structure file in PDB format.
  • select all or any of the required job.
  • can change the default threshold values as per requirement.
  • Hit the "Go" button to initiate the calculations.

4.OPTIONS

• The options available are:
  
  
  1. Protein properties
  
  a. Molecular weight.
  b. Atomic composition.
  c. Amino-acid composition.
  d. Theoretical isoelectric point.
  e. Estimated half-life.
  f. Extinction coefficient and Absorbance.
  g. Solubility.
  h. Aliphatic index.
  i. Grand Average of Hydropathicity (GRAVY).
  
  
  
  2. Center of Mass
  
  a. Add Hydrogens to the input file.
  b. With consideration of heteroatoms.
  c. Without considering heteroatoms.
  
  
  
  3. Intra-protein Interactions
  
  a. Disulfide Bridges.
  b. Ionic Interactions.
  c. Hydrophobic Interactions.
  d. Hydrogen Bond Interactions.
  e. Aromatic-Aromatic Interactions.
  f. Aromatic-Sulphur Interactions.
  g. Cation-Pi Interactions.
  h. Electrostatic interactions.
  

5.OUTPUT

• The output of protein interactions lists positions and chains of the interacting residues along with the inter-atomic distances and angles.
  
  Distinct features of PIPE output
  
  1. Optional addition of Hydrogens to the input PDB file for COM calculation.
  2. Calculation of various Basic Protein Properties.
  3. Pie chart view of Atomic composition.
  4. Interactive bar graph for Amino Acid Composition.
  5. Jmol display is used for
  

  a. COM (center of mass) position.
  b. highlighting the nature of residues.
  c. various possible interactions among residues.
  

  6. Detailed tabular view also available for all types of interactions.
  7. Provides the list of the missing residues and atoms in the input PDB file.
  
  
  

  6. Login to Workspace

• Login is required to retrieve the previous results which requires a valid E.mail id. PIPE server will save your results for a period of seven days.