Bioinformatics Tools

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====== Protein - ligand interaction ====== [[https://projects.biotec.tu-dresden.de/plip-web/plip/index | PLIP:]] Protein-Ligand Interaction Profiler [[http://poseview.zbh.uni-hamburg.de/poseview | Poseview on-line]] [[http://www.biochem.ucl.ac.uk/bsm/ligplot/ligplot.html | LIGPLOT:]] Program for automatically plotting protein-ligand [[http://mespeus.bch.ed.ac.uk/MESPEUS/ | MESPEUS:]]Metal Sites in Proteins - MESPEUS database [[http://dicsoft2.physics.iisc.ernet.in/cgi-bin/mips/query.pl | MIPS:]]Metal Interactions in Protein Structures [[http://www.charmm-gui.org/?doc=input/gbinding | The Ligand Binder:]] helps the user generate a series of CHARMM inputs to calculate a protein/ligand binding free energy. [[http://www.biosolveit.de/PoseView/ | PoseView:]] automatically generates high-quality 2D structure-diagrams of protein-ligand complexes provided as 3D-input. Such input may come directly from crystal structures or be computed for example by a docking program. [[http://metalweb.cerm.unifi.it/ | MetalPDB]] collects and allows easy access to the knowledge on metal sites in biological macromolecules, starting from the structural information contained in the Protein Data Bank (PDB) [[http://proline.physics.iisc.ernet.in/pocketmatch/ | Pocketmatch:]]Usage of this web interface: Two PDB files whose ligands need to be compared are obtained from the upload. Each of the protein files is then processed to extract all ligands and their corresponding site files. All vs All comparison of sites is done with PocketMatch and scores are reported. ====== Protein - Protein interaction ====== [[http://pipsa.eml.org/pipsa/pdbupload | webPIPSA:]] Protein Interaction Property Similarity Analysis ====== List of other servers ====== [[https://bioinformatictools.wordpress.com/tag/metapocket/ | list]] of software of pocket characterization