The simulation software package Molden (MOLecular DENsity), which has been and is developed by G.Schaftenaar. This simulation software is used in hundreds of laboratories in countries on all continents. Address: http://www.cmbi.ru.nl/molden
Rotacal is a package for searching the rotameric space of a proteins active site. It is being developed by master student Aleks Depta, with contributions from Joep de Ligt (dfire potential) and master student Bas Vroling (representation of MD frames by rotameric ‘sequences' )
PhyloPat is an easy-to-use webserver, which can be used to query the orthologies of all complete genomes within the EnsMart database using phylogenetic patterns. This enables the determination of sets of genes that occur only in certain evolutionary branches or even single species. We found in total 815,452 genes and 17,332,165 orthologous relationships within the EnsMart v49 database. We used a single linkage clustering algorithm to create 241,697 phylogenetic lineages, using every one of the orthologies provided by Ensembl. PhyloPat provides the possibility of querying with either binary phylogenetic patterns (created by checkboxes) or regular expressions. Specific branches of a phylogenetic tree of the 39 included species can be selected to create a branch-specific phylogenetic pattern. Users can also input a list of Ensembl, EMBL, or HUGO IDs to check which phylogenetic lineage any gene belongs to. The output can be saved in HTML, Excel or plain text format for further analysis. A link to the FatiGO web interface has been incorporated in the HTML output, creating easy access to functional information. Furthermore, lists of omnipresent, polypresent, oligopresent and anticorrelating genes have been included. Finally, clicking on a PhyloPat ID will show the gene neighborhood for all genes in that phylogenetic lineage. Address: http://www.cmbi.ru.nl/phylopat
CoPub is a text mining tool that detects co-occuring biomedical concepts in abstracts from the MedLine literature database. The biomedical concepts included in CoPub are all human, mouse and rat genes, furthermore biological processes, molecular functions and cellular components from Gene Ontology, and also diseases, drugs and pathways. Altogether more than 260,000 search strings are linked with CoPub. Special attention was given to genes and proteins. For all human, mouse and rat genes not only long forms of names were used, but also their symbols and aliases, which increases recall. Symbols not referring to genes or proteins are a well known problem, but sophisticated scripts detect these homonyms and neglect the abstracts in which they occur thereby increasing precision. CoPub is especially useful for microarray data analysis. It is often difficult to grasp the meaning of lists of differentially expressed genes. Mining MedLine with gene names one by one is laborious and tedious, if not impossible, and many relevant abstracts will be missed. With CoPub it is now possible to upload a list of Affymetrix identifiers and find biomedical concepts from MedLine that are significantly linked to the gene set. From every retrieved biomedical concept it is only one mouse click to copublished genes and another one to the relevant abstracts. CoPub is hosted and further developed by SARA and is made available at CoPub.
BioVenn is an easy-to-use web application to generate area-proportional Venn diagrams from lists of biological identifiers. It supports a wide range of identifiers from the most used biological databases currently available. Its implementation on the World Wide Web makes it available for use on any computer with internet connection, independent of operating system and without the need to install programs locally. BioVenn is freely accessible at http://www.cmbi.ru.nl/cdd/biovenn
Fleksy is a new approach to consider both ligand and receptor flexibility in small molecule docking. Pivotal to the method is the use of a receptor ensemble to describe protein flexibility. To construct these ensembles, we use a backbone-dependent rotamer library and implement the concept of interaction sampling. The latter allows the evaluation of different orientations of ambivalent interaction partners. The docking stage consists of an ensemble-based soft-docking experiment using FlexX-Ensemble, followed by an effective flexible receptor-ligand complex optimization using Yasara. Fleksy produces a set of receptor-ligand complexes ranked using a consensus scoring function combining docking scores and force field energies.