Wednesday, 13 April 2011

Splicing isoforms modeling, peptidomimetics and molecular dynamic made easy

This new season is started with 3 new accepted papers. Here a brief introduction, I will give more details very soon for each of them:

  1. MaƬstas (Bioinformatics, first name), a fully automatic pipeline aimed at building and assessing three-dimensional models for alternative splicing isoforms. The server builds, when possible, comparative structural models for all the splicing isoforms of a submitted gene or set of genes. The models are then analysed in terms of their suitability to exist in the monomeric state, i.e. when a warning appears in the model assessment, it cannot be excluded the possibility that other multimeric state may stabilize the structure. Moreover, the splicing isoform exonic coordinates are mapped on the final models.
  2. pep:MMs:MIMIC (Nucleic Acid Research, Web Server Issue, first name), a web-oriented tool that, given a peptide three-dimensional structure, is able to automate a multiconformers three-dimensional similarity search among 17 million of conformers calculated from 3.9 million of commercially available chemicals collected in the MMsINC database.
  3. ClickMD (Future Medicinal Chemistry), a web-based explicit solvent molecular dynamic simulator. ClickMD performs minimization, equilibration phase and a short run of classical MD. ClickMD works with PDB files of protein and peptides. You just needs a valid PDB file to start the MD simulation! You will receive an e-mail at the end of the simulation containing a link to a web page where you can download the MD results as: log files, trajectory files, energy and RMSD representations and graphs.


  1. This comment has been removed by a blog administrator.

  2. It was a awe-inspiring post and it has a significant meaning and thanks for sharing the information.Would love to read your next post too......


    ISO 9001