Software

Most of the structures and function of globular domains from the proteome are yet unknown. In order to get some information about the biological role of these domains, the development of a methodology for the modelling, prediction and localization of putative partners is of crucial importance since it can be of general applicability for any domain involved in protein-protein interactions.

ADAN is a database of putative ligands for the most well-known modular protein-protein interaction domains like SH3, PDZ, etc. Many of these domains have a large number of homologues of which only a small fraction has been crystallized and only limited number of ligands is known. Based on the known structures, the ADAN project creates full atomic models of unknown protein-ligand structures using the FoldX algorithm and predicts new putative binders. A querying function allows the user to input a polypeptide sequence and retrieve the putative binding segments for a particular domain.

ADAN results from the collaboration between the group of Luis Serrano, currently at the CRG in Barcelona and Gregorio Fernández, researcher from the Cellular and Molecular Biology Institute of the Miguel Hernández University in Elche, Alicante.

Agadir is a prediction algorithm based on the helix/coil transition theory. Agadir predicts the helical behaviour of monomeric peptides. It only considers short range interactions. Conditions such as pH, temperature and ionic strength are used in the calculation. Modifications of the termini are also allowed. Agadir is not a program to predict secondary structure of proteins.

AStalavista, the Alternative Splicing Trascriptional Landscape Visualization Tool and more, retrieves all alternative splicing events from generic transcript annotations.

BriX is a structural classification of protein fragments. The library comprises fragments ranging from 4 to 14 amino acids that are clustered against 6 different distance thresholds. This has lead to an alphabet of around 2000 frequently observed letters or structural classes per chain length. These classes are accessible through a search and a browse interface.

BriX is being developed by Joost Schymkowitz and Frederic Rousseau and their team at the SWITCH Laboratory of VIB in Brussels, Belgium, in collaboration with Luis Serrano and his team at the CRG in Barcelona, Spain.

For more information about this software, please click here.

We have developed a tool which derives gene-specific estimates of the strength of negative and positive selection in cancer. It accounts for the heterogeneity of mutation rate across the cancer genome, independent of external input information on mutation rate covariates. CBaSE estimates also take into account the context-dependent cancer type-specific mutational signature.

The CBaSE method and results were published in Weghorn & Sunyaev, Nature Genetics, 2017:
https://www.nature.com/articles/ng.3987.epdf

The CBaSE software can be downloaded as a standalone tool or used in a browser-based application here:
http://genetics.bwh.harvard.edu/cbase/index.html

catRAPID is an algorithm to estimate the binding propensity of protein-RNA pairs. By combining secondary structure, hydrogen bonding and van der Waals contributions, catRAPID predicts protein-RNA associations with great accuracy.

ccSOL omics allows fast and accurate large-scale predictions of protein solubility. The algorithm exploits a list of physico-chemical scales, such as hydrophobicity/hydrophilicity, coil/turn/disorder and alpha-helix to compute propensity profiles for each protein.

Two lists of proteins are compared using physicochemical features (e.g., hydrophobicity, RNA-binding propensities etc). The differential analysis is used to build models for the cleverClassifier

compmerge is a program that tries to solve the same problem as cuffmerge. It is not limited to cufflinks/stringtie models and transcripts, but can work with any GTF file. It merges the spliced transcripts that have a compatible intron structure and merges the monoexonic transcripts based on simple stranded overlap.The output is a GTF file of merged transcripts.

Given a 3'UTR sequence, the CPE-mediated translational control web server predicts the class of translational control behavior the corresponding mRNA belongs to.
The classification is done according to the combinatorial code for translational regulation discovered by Pique et al.

CRISPETa is a flexible tool to design optimal pairs of sgRNAs for deletion of desired genomic regions. These target regions can be supplied in BED or UCSC format. CRISPETa can be run on any number of targets - from one to thousands.

Deathbase is a database of proteins involved in cell death. It compiles relevant data on the function, structure and evolution of proteins involved in apoptosis and other forms of cell death in several organisms. Information contained in this database is subjected to manual curation. You can contribute to maintain the DeathBase by editing the wikipage for any protein.

The transcriptome project aims to sequence various cell lines, and within those cell lines, different compartments, and RNA fractions, using different technologies.

ETE (Environment for Tree Exploration) is a python programming toolkit that assists in the automated manipulation, analysis and visualization of hierarchical trees. Besides a broad set of tree handling options, ETE’s current version provides specific methods to analyze phylogenetic and clustering trees. It also supports large tree data structures, node annotation, independent editing and analysis of tree partitions, and the association of trees with external data such as multiple sequence alignments or numerical matrices. ETE first version was developed in collaboration with Dr. Joaquín Dopazo lab at Centro de Investigación Príncipe Felipe (CIPF).

FoldX is a computer algorithm developed to provide a fast and quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes. The predictive power of the algorithm has been tested on a very large set of point mutants spanning most of the structural environments found in proteins, as well as on protein complexes and protein-DNA complexes of medical and biotechnological relevance. FoldX uses a full atomic description of the structure of the proteins. The different energy terms taken into account in FoldX have been weighted using empirical data obtained from protein engineering experiments.
FoldX is being developed by the group of Luis Serrano at the CRG in Barcelona, Spain, in collaboration with Joost Schymkowitz and Frederic Rousseau and their team at the SWITCH Laboratory of VIB in Brussels, Belgium.