Resources

Features:

ADSBET is the fully automated single step procedure that takes crystal structure as input and redirect salt-bridge energies as output in excel format i.e.

1. Net interaction energy as well as component energies such as, a) bridge-term b) background or protein term c) desolvation term

2. It runs from CYGWIN or other UNIX like environment

3. It is fast, accurate and user-friendly tools that works on any number of crystal structures with any number of salt-bridges in them.

4. Most importantly ADSBET does not involve any manual step (although there were many for such computations)

​

​

Features:

ADSBET is the fully automated single step procedure that takes crystal structure as input and redirect salt-bridge energies as output in excel format i.e.

1. Net interaction energy as well as component energies such as, a) bridge-term b) background or protein term c) desolvation term

2. It runs from CYGWIN or other UNIX like environment

3. It is fast, accurate and user-friendly tools that works on any number of crystal structures with any number of salt-bridges in them.

4. Most importantly ADSBET does not involve any manual step (although there were many for such computations)

​

​

Features:

1. SBION2 can process any number of structures with .pdb extension

2. Chains ----- all chains in structures

3. Salt bridge(sb) distance ----- user choice

4. Local threshold ----- user choice

5. Core threshold ----- user choice

6. Ugly PDBs ----- corrected

7. NMR files ----- screened out

8. Missing residue ----- reported

9. sb distance ----- averaged over sb partners interactions

10. Binary outputs ----- in excel format

​  Read more........

Features:

• SBS Energy-terms in general [kcal/mol] and normalized [kcal/mol/bond] format, Only the LATER is comparable among SBSs and hence help for their statistical analyses.

• Combines energy terms in NSBS and ISBS format; NSBS-> Networked SBS forms - 1:2 [dimer], 1:3 [trimer] etc.; NSBS types-> i.e. base-networked SBS and acid networked SBS; ISBS- Isolated SBS form - 1:1 form[monomer]

• Accessible surface area i.e. ASA in NSBS and ISBS form; the program uses SURFACE-RACER [option 4] /POPS [option 5] /NACCESS option 6]

• ddGprot [hence ddGnet] in two categories based on source of charges; ddGprot-I: partial charges due to all-sides [Nayek et al, 2014]; ddGprot-II: Partial charges due to acidic and basic residues [Kumar and Nussinov, 1999]

Features:

ADSBET is the fully automated single step procedure that takes crystal structure as input and redirect salt-bridge energies as output in excel format i.e.

1. Net interaction energy as well as component energies such as, a) bridge-term b) background or protein term c) desolvation term

2. It runs from CYGWIN or other UNIX like environment

3. It is fast, accurate and user-friendly tools that works on any number of crystal structures with any number of salt-bridges in them.

4. Most importantly ADSBET does not involve any manual step (although there were many for such computations)

​

​

Features:

A fully automated procedure that can analyze a large database of crystal structures with variable number of chains in them , for the results of absolute and normalized compositions of the core, surface and rim of any number of x-ray structures with any number of chains in them.

1. Automated procedure that can analyze a large database of crystal structures with variable number of chains in them.

2. Results of absolute and normalized compositions of the core, surface and rim of any number of x-ray structures with any number of chains in them.

3. It redirects two outputs: one for single PDB (useful for individual analysis) and other for all PDBs (useful for statistical analysis).

​

​

Features:

• PHYSICO2 (version 2.0) – It is improved version of our earlier program (PHYSICO: Gupta et al Bioinformation, 10(2), 105-107, 2014) and an automated standalone, multipurpose procedure for analysis of protein se-quences in FASTA format. The program works from UNIX like environment including CYGWIN1 and is interpreted by AWK programming language. It can works on various forms of FASTA files (Input). Based on the form of FASTA-input, relevant outputs are produced. The program is designed such that large database of sequences can be ana-lyzed in a single run. Overall, it provides countable advantages over the existing web-tools. Read more.......

​

Features:

• Computes the propensity tables for helix, sheet and coil types from multiple 3D structure files following ab initio statistical procedure.

• Incorporate %-composition and physicochemical properties along with residues propensities.

• Prepares FASTA files for different segments (Helix, Strand and Coil) following exact order of their presence in the entire sequence.

​