bazy_notatki

Moje notatki

• http://www.rcsb.org/pdb/101/static101.do?p=education_discussion/Looking-at-Structures/methods.html
• http://www.moleculardescriptors.eu/dataset/dataset.htm - bazy danych do QSARu

Ciekawe narzędzia

• baza danych związków chemicznych: http://www.ambinter.com/moleditor/web/learn-more (A free software to create, edit and export a simple chemical database online)

Dokowania

• a procedure to customize the box size for individual query ligands in order to maximize the accuracy of molecular docking: http://brylinski.cct.lsu.edu/content/docking-box-size

• reduce reduce.3.23.130521.linuxi386 - http://kinemage.biochem.duke.edu/software/reduce.php :: Reduce is a program for adding hydrogens to a Protein DataBank (PDB) molecular structure file. Hydrogens are added in standardized geometry with optimization of the orientations of OH, SH, NH3+, Met methyls, Asn and Gln sidechain amides, and His rings. Both proteins and nucleic acids can be processed. HET groups can also be processed as long as the atom connectivity is provided.

• idock: /~https://github.com/HongjianLi/idock (ale się nie kompiluje)

• rdock

Inne

• generowanie konformacji: Multiconf-DOCK - ready to use

• http://dunbrack.fccc.edu/scwrl4/ - SCWRL 4.0, as Stephane suggested. Optimize the mutated residues and all contacting residues, leave the rest untouched

Publikacje

Stefaniak F (2015). Prediction of compounds activity in nuclear receptor signaling and stress pathway assays using machine learning algorithms and low dimensional molecular descriptors. Front. Environ. Sci. 3:77. doi: 10.3389/fenvs.2015.00077

Zupełnie inne

• https://asciinema.org/ - nagrywanie sesji terminalowej.

To fetch

• Exploring RNA oligomerization and ligand binding by fluorescence correlation spectroscopy and small angle X-ray scattering