support cutting-edge research and experimentation
Advanced Tools
- Published software
- afal2: This application uses the protein data bank (PDB) to acquire detailed structural information (amino acids interaction, distances between the ligand and the amino acids) about the interactions between a given ligand and its binding sites in different proteins. The program searches for and analyses all structures in the PDB containing this particular molecule to determine which amino acids are involved in binding. https://structuralbio.utalca.cl/afal2/
- mutanelec: Is a Web application for in silico generation of site-directed mutagenesis of proteins and the comparation of electrostatic potential between the wild type protein and the mutant. https://structuralbio.utalca.cl/mutantelec/
- gsp4pdb: Is a web tool that lets the users visualize, search and explore protein-ligand structural patterns inside the Protein Data Bank. http://gdblab.com/gsp4pdb/gsp4pdb2/
- geomfinder: An intuitive, flexible and ligand-independent web server for detailed estimation of similarities between all pairs of 3D patterns detected in any two given protein structures. http://geomfinder.appsbio.utalca.cl
- 3d-pp: A web server for discovering and recognition all similar 3D amino acid patterns among a set of proteins structures (independently of their sequence similarity). http://3d-pp.appsbio.utalca.cl
- LigRMSD: A web server for automatic structure matching and RMSD calculations among identical and similar compounds in protein-ligand docking. https://ligrmsd.appsbio.utalca.cl/
- PSC-DB (Plant Secondary Compound DataBase): Is a free accessible database containing the 3D-structures of the most relevant Plant Secondary Compounds along with its physicochemical and pharmaceutical properties. http://pscdb.appsbio.utalca.cl/
- Under development
- Geomfinder2 (parallelized/optimized version): http://geomfinder2.appsbio.utalca.cl
- bsfinder: A database storing the binding sites detected by the Fpocket program. http://bsfinder.appsbio.utalca.cl
- cchain: A tool to concatenate chains. http://cchain.appsbio.utalca.cl
- TEcandidates: Is a pipeline to include transposable elements in RNA-seq differential expression analysis. https://www.mobilomics.org/tecandidates/
- TnpPred: Is a web service for the prediction of Prokaryotic transposases based on 47 validated Hidden Markov Models (HMM profiles) for 19 Insertion Sequence transposase families. https://www.mobilomics.org/software/tnppred/tnppred.php
- HMMTeacher: Is a tool that teaches interactively how Hidden Markov Models work. This tool divides the modeling into a sequence of steps that leads the user to the final solution of the problem. https://hmmteacher.mobilomics.org/
- High-Performance Computing Infrastructure
CPU Clusters
- HP Blade BL420C – 1 Headnode, 32 nodes, 256 Core CPU, 8 cores CPU 8 GB RAM per node.
- Ethernet 1Gbps e Infiniband 10Gbps.
- HP Generic – 1 Headnode, 12 nodes, 192 Core CPU, 32 GB per node.
- Ethernet 1Gbps e Infiniband 52Gbps.
GPU Clusters
Total 8 Nodes 64 GPU – 128 CPU.
6 Nodes:
- 48 Nvidia Geforce Titan X Pascal
- 12 x Intel® Xeon® processor E5-2620 v4, 8C, 2.1 GHz.
2 Nodes:
- 16 Nvidia Tesla k80 24 GB
- 4 x Intel® Xeon® processor E5-2620 v4, 8C, 2.1 GHz 20M, 85W.
