https://academic.oup.com/nar/search-results?f_TocHeadingTitle=Web%20Server%20issue

1. PPI   PIZSA http://cospi.iiserpune.ac.in/pizsa

2. Nucleic acid (NA) docking for RNA/DNA-RNA/DNA complex structure modeling http://huanglab.phys.hust.edu.cn/hnadock/

3. Drug ReposER: a web server for predicting similar amino acid arrangements to known drug binding interfaces for potential drug repositioning

http://mfrlab.org/drugreposer/

4. HawkDock: a web server to predict and analyze the protein–protein complex based on computational docking and MM/GBSA

http://cadd.zju.edu.cn/hawkdock/

5. SwissTargetPrediction: updated data and new features for efficient prediction of protein targets of small molecules  (www.swisstargetprediction.ch).

6.MERMAID: dedicated web server to prepare and run coarse-grained membrane protein dynamics

 The MERMAID server is equipped with the web interface written in HTML 4/5 (https://www.w3.org/html/), PHP (http://www.php.net/), JavaScript (https://www.javascript.com/), Bash shell (https://www.gnu.org/software/bash/), jQuery (https://jquery.com/), and Bootstrap 4 (https://getbootstrap.com/). For the submitted jobs, the web server prepares MERMAID input files on our local cluster. At last, the results are post-processed (which includes analysis of CGMD trajectory, construction of various data plots) and displayed graphically by using Highcharts (https://www.highcharts.com/) and Plotly (https://plot.ly). The web server can be accessed from any media device and the jobs can be monitored and followed up 

7. VoroMQA web server for assessing three-dimensional structures of proteins and protein complexes

http://bioinformatics.ibt.lt/wtsam/voromqa.

8.AppA: a web server for analysis, comparison, and visualization of contact residues and interfacial waters of antibody–antigen structures and models  http://mspc.bii.a-star.edu.sg/minhn/appa.html

9. AlloDriver: a method for the identification and analysis of cancer driver targets http://mdl.shsmu.edu.cn/ALD.

10 DrugComb: an integrative cancer drug combination data portal 

11. MAFFT-DASH: integrated protein sequence and structural alignment  (https://mafft.cbrc.jp/alignment/server/) 

12. IntFOLD: an integrated web resource for high performance protein structure and function prediction

  http://www.reading.ac.uk/bioinf/IntFOLD/.

13. Identification and visualization of protein binding regions with the ArDock server ArDock (ardock.ibcp.fr)

13.  cgDNAweb : a web interface to the cgDNA sequence-dependent coarse-grain model of double-stranded DNA 

14. COACH-D: improved protein–ligand binding sites prediction with refined ligand-binding poses through molecular docking

15.gRINN: a tool for calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations  http://grinn.readthedocs.io.

16.HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information http://loschmidt.chemi.muni.cz/hotspotwizard. 

17. ComplexContact: a web server for inter-protein contact prediction using deep learning (http://raptorx2.uchicago.edu/ComplexContact/) sequence-based interfacial residue-residue contact prediction

18. GPCRM: a homology modeling web service with triple membrane-fitted quality assessment of GPCR models 

19.CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures  http://biocomp.chem.uw.edu.pl/CABSflex2. 

20. CavityPlus: a web server for protein cavity detection with pharmacophore modelling, allosteric site identification and covalent ligand binding ability prediction The CavityPlus web server is freely available at http://repharma.pku.edu.cn/cavityplus or http://www.pkumdl.cn/cavityplus.

21. HPEPDOCK: a web server for blind peptide–protein docking based on a hierarchical algorithm  http://huanglab.phys.hust.edu.cn/hpepdock/.

22. INTERSPIA: a web application for exploring the dynamics of protein-protein interactions among multiple species  http://bioinfo.konkuk.ac.kr/INTERSPIA/.

22. InterEvDock2: an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs  at http://bioserv.rpbs.univ-paris-diderot.fr/services/InterEvDock2/.

23. DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability http://biosig.unimelb.edu.au/dynamut/.

24.  HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy  http://hdock.phys.hust.edu.cn/.

25. AMMOS2: a web server for protein–ligand–water complexes refinement via molecular mechanics http://drugmod.rpbs.univ-paris-diderot.fr/ammosHome.php.

26. PharmMapper 2017 update: a web server for potential drug target identification with a comprehensive target pharmacophore database http://lilab.ecust.edu.cn/pharmmapper/.

27. ModFOLD6: an accurate web server for the global and local quality estimation of 3D protein models http://www.reading.ac.uk/bioinf/ModFOLD/.

28. GASS-WEB: a web server for identifying enzyme active sites based on genetic algorithms http://gass.unifei.edu.br/.

29. LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands 

30.ReFOLD: a server for the refinement of 3D protein models guided by accurate quality estimates  http://www.reading.ac.uk/bioinf/ReFOLD/.