Projects

coot

Coot is a suite of programs for macromolecular model-building using X-ray data incorporating interactive molecular graphics including refinement, rebuilding and model validation. Coot is built on top of several layers, including the GNU Scientific Library, GTk, Guile, guile-gtk, coordinate ... [More] handling libraries (mmdb), crystallographic object handling libraries (clipper), GNOMECanvas and OpenGL. [Less]

GNAT NER

GNAT is a library and web service capable of performing gene entity NER and normalization of biomedical articles. Mentions of genes and proteins in the articles are linked to to Entrez Gene identifiers. GNAT is available both for local download (suitable for large-scale processing) and as a web ... [More] service (suitable for more limited processing or testing). A combination of local and remote processing is also available, where CPU-heavy operations are performed locally and memory-intensive operations are performed remotely (this is suitable for large-scale processing where a large amount of memory is not available). GNAT uses LINNAEUS (Gerner et al., 2010) for species detection and BANNER (Leaman et al., 2008) in one part of its false positive filtering process. [Less]

ncbi

This is a software that helps you to search the Ncbi Website(Enterz Databases) for your specific query making the fuss a lot simpler. All you have to do is select the type of search you want to do like on proteins or nucleotide or 3D domains or 3d structures or gene or dna or structure or gnome,etc ... [More] and type in the name or the keyword you want to get the information for and it fetches the result for you. Genome specific researches can be carried out.Est databases can now be accessed without any hassle. It is faster over the conventional web browser method. Two or more results ca be compared at the same time with the help of a Desktop Pane The Software is available under the GNU GPL V3 [Less]

PAML

PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang. ANSI C source codes are distributed for UNIX/Linux/Mac OSX, and executables are provided for MS Windows. PAML ... [More] is not good for tree making. It may be used to estimate parameters and test hypotheses to study the evolutionary process, when you have reconstructed trees using other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc. (from the PAML website) [Less]

pconpy

PConPy is an open-source Python module for generating publication-quality protein contact maps, distance maps, and hydrogen-bond plots. PConPy can be used as a standalone application or as an extension to existing source code. The maps generated by PConPy are vectorised and can therefore be scaled ... [More] without loss of image quality for use in publications, presentations, or analyses. Users also have the option to generate maps in raster image formats. [Less]

aquad

AQUA is a suite of programs for Analyzing the QUAlity of biomolecular structures that were determined via NMR spectroscopy. AQUA was developed by Ton Rullmann and Jurgen Doreleijers in the NMR Spectroscopy Department, Utrecht.

stransmem

Signals to be passed to cells either pass the plasma membrane (like for instance some hormones with receptors in the nucleus) or they are sensed on the cellular surface by membrane proteins (olfaction, inflammation, ..., the presumed majority of sensory events). Albeit frequently overseen in ... [More] biological and particularly bioinformatical considerations, many transmembrane proteins have soluble variants. There are plenty of non-sensatory biological processes that involve membrane proteins, but these aside, it is particularly intuitive to think of such soluble variants as competitive binders to ligands that cannot induce intracellular cascades (e.g., the soluble receptor for TNF alpha). In other cases, the soluble variant itself is the signal (e.g., TNF alpha itself). This project presents a dataset of soluble membrane proteins that were collected from the literature. It shall become the basis for future efforts of the computational biology community to find patterns in sequence or structure that might allow for the prediction of the existence of a soluble variant. The data is organized in an XML file and allows, if known, the distinction between solubilization that is induced by alternative splicing and such that resulted from proteolytic cleavage by a protease. [Less]

iself

Self assembly of patchy colloidal polymers

popitam

Popitam is a method designed to characterize peptides with mutations or unexpected post-translational modifications using MS/MS data.

ppi-project

Mostly matlab code. Interactions are predicted using domain to domain interaction information, as well as hidden Markov models and support vector machines.