Structure visualization softwares

Chimera:
https://www.cgl.ucsf.edu/chimera/

Open structure:
http://www.openstructure.org

Structure modelling

Swiss-modeller
http://swissmodel.expasy.org/

Modeller
https://salilab.org/modeller/

Modip: Stereochemical modelling of disulfide bridges
http://caps.ncbs.res.in/iws/modip.html

Electrostatic potential surface calculator

PDB2PQR-APBS server
http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/

Protein structure database search

DALI server
http://ekhidna.biocenter.helsinki.fi/dali_server/start

Protein Interactions Calculator

P I C : Protein Interactions Calculator
http://pic.mbu.iisc.ernet.in/

Protein structure model minimization

Chiron: Rapid Protein Energy Minimization Server
http://troll.med.unc.edu/chiron/login.php
Yasara Energy Minimization Server
http://www.yasara.org/minimizationserver.htm
KobaMin - Knowledge-based Potential Refinement for Protein
http://csb.stanford.edu/kobamin/

Side-chain generator for PDB with only CA

REMO : From C-alpha Trace to Full-atom Model
https://zhanglab.ccmb.med.umich.edu/REMO/

Protein-protein docking simulation

Rosetta Online Server that Includes Everyone [ROSIE]
http://rosie.rosettacommons.org/

ClusPro protein-protein docking
https://cluspro.bu.edu