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HORI - Server to compute Higher Order Residue Interactions in proteins - Help Page:

HORI SERVER - Help Index:

1. Introduction
2. List of programs available in HORI Server
3. HORI Server Statistics
4. Enter your valid E-mail ID
5. Upload Your PDB File
6. Select Atom type for Distance Calculations (C-α or C-β)
7. Select Interaction Type
8. Enter Distance Cut-off
9. Enter Chain ID
10. Precomputed Results from HORI Server
11. Example Run - Try and use HORI Server in easy steps
12. HORI Server - Browser Compatability

1. HORI-Server Introduction:

HORI is a web server to compute higher order residue interactions in protein structures. HORI offers a set of programs to calculate Pairwise, Triplet and Quadruplet interactions with in the protein structures.


Figure 1 : Graphical representation of individual Higher order residue interactions mapped on to Crambin (PDB ID: 1CRN)

HORI Server is designed as three modules :

  • HORI-Global : Complete structure level computation of different higher order residue interactions
  • HORI-Lite : Specific higher order residue interaction computation based on residue numbers in input PDB files
  • HORI-Cluster : Higher order residue interaction computation based on residue types in input PDB files

HORI-Global offers 2 programs for computationaly intensive calculation of Pairwise, Triplet and Quadruplet interactions in the protein structures. HORI-Lite and HORI-Clusters offers a set of 9 programs for comparatively quick calculations of specific/generic interactions with in protein structures. HORI-Global, HORI-Lite and HORI-Cluster computations can be performed using C-α or C-β based distance calculation methods. Easy-to-use web interfaces are available for all programs in HORI server to calculate using single chain and multichain proteins (2 chains at a time).


2. List of programs available in HORI Server:
In HORI-Global:
  • Compute Higher Order Residue Interactions for Single Chain & Multi Chain Proteins (Complete structure based calculation -Pairwise, Triplet and Quadruple Interactions)
  • Compute Higher Order Residue Interactions for Single Chain & Multi Chain Proteins (Residue range based - Pairwise, Triplet and Quadruple Interactions)
In HORI-Lite & HORI-Cluster:
  • Compute Pairwise Distance for any 2 residues in PDB file (Pairwise Interactions)
  • Compute Pairwise Distance around any 1 residues in PDB file (Pairwise Interactions)
  • Compute Triplet Distances between any 3 residues in a PDB file (Triplet Interactions)
  • Compute Triplet Distances around any 2 residues in a PDB file (Triplet Interactions)
  • Compute Triplet Distances around 1 residue (Triplet Interactions)
  • Compute Quadruple Distances between any 4 residues in a PDB file (Quadruple Interactions)
  • Compute Quadruple Distances around any 3 residues in a PDB file (Quadruple Interactions)
  • Compute Quadruple Distances around 2 residues in a PDB file (Quadruple Interactions)
  • Compute Quadruple Distances around 1 residue in a PDB file (Quadruple Interactions)

NB. HORI-Lite and HORI-Cluster offers similar set of programs for the computations, but the input options are different.
Interaction types are available for each program as it is given in brackets.

3. HORI Server Statistics:
ModuleSingle Chain / Multi-ChainNo. of Programs
  HORI-Global   Both 2
  HORI-Lite   Both 9
  HORI-Cluster   Both 9

4. Enter your valid E-mail ID:

HORI-Global is a computationally intensive module that requires considerable amount of time for computation of complete structure level higher order interactions. Hence we designed this particular module as email based server, wher user should provide a valid email ID for the submission and process. Please enter your valid email ID (preferably academic email ID) to receive HORI-Global results. Check your email address for any 'typos' before submitting the HORI process to the server. We remind the users that "HORI-Global is using a computationally internsive protocol", so please provide a valid email address for the secure delivery of your results.


5. Upload PDB File:

HORI server requires a PDB file as its input for the computation of higher order residue interactions. HORI Server provides separate interface for single chain and multi chain proteins. If you would like to submit an NMR structure , Please submit Chain IDs of two chains at a time in multi-chain based programs. Due to computational intense nature of HORI calculations, currently the server will accept only two chain for calculation. Users may remove HETATM / ANISOU records from the PDB Files.

  • HORI Server can perform computations on exprerimentatlly (X-ray, NMR) solved structures as well as modelled strucutures using softwares like MODELLER, SWISSMODEL,SCWRL in PDB format.
  • Submit either single chain of interest from an NMR based PDB file as input in Single-chain based programs or enter the chain IDs of any two chains in mult-chain based programs.
  • Please note that HORI server will not consider HETATM/ANISOU records in the input file during calculations, only records tagged as ATOM will consider for computation.
  • In HORI-Lite, Please specify the residue numbers present in the given input PDB file for various computations.
  • In HORI-Cluster, Please specify the residue types that are present in the given input PDB file for various computations.

6. Select Atom type for Distance Calculations (C-α or C-β):

HORI Server offers wide array of programs for the computation of higher order residue interactions. All computations in HORI server can be performed using two distance parameters C-α or C-β atom type. Atom type for distance calculation is available as an option, so that user can decided the atom type for distance calculation.


7. Select Interaction Type:

HORI-Global offers different options to compute higher order residues interactions in protein structure. Users can select any of the 4 options provided in the HORI-Global. The Interaction type options are Pairwise, Triplet, Quadruplet and All. Here 'All' indicates computation using all three interatction types available in HORI-Global.


8. Enter Distance Cut-off:

HORI calculations are distance dependent, users can specify the distance cut-off for the calculations. Users can enter any number between 0-14, it is highly recommended to perform HORI computations with in a reliable distance of 7 Angstroms. For example Lower Limit: 0 and Upper Limit: 7. Distance cut-off is one of the major parameter in HORI server to identify residues interacting in higher orders like pairwise, triplet and quadruple.


9. Enter Chain ID:

HORI offers different web interfaces for HORI calculations for single chain and multi-chain structures. Multi-chain option will be useful for the users interested to perform the HORI computations on higher oligomers. Due to limitation of computation, current version of HORI multi-chain programs perform computation using only two chains at a time. Users uploading multi-chain (PDB files with 2 or more chains) should enter their chain ids for the successful HORI computation. Different options are available in different groups of HORI server to mention the residue number/type along with chain ID.


13. HORI Server - Browser Compatability:
We tested different browsers in different operating systems to assess the compatibility of HORI server.
We recommend the users to use the respective browsers for the optimum perfomance of HORI server.
Flavours of Linux : Firefox
Microsoft Windows® : Firefox, Safari
Mac OS® : Firefox, Safari

Contact:
Prof. R. Sowdhamini (mini@ncbs.res.in)

HORI Server Team : P. Sundaramurthy, Raashi Srinivasan, K. Shameer, Prof. Sunita Gakkhar & Prof. R. Sowdhamini