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Protein Evolution (Rob Russell)Protein Evolution Heidelberg, Prof. Rob Russell
http://dilimot.russelllab.org/
Protein Evolution Heidelberg, Prof. Rob Russell
http://dilimot.russelllab.org/
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Protein Evolution (Rob Russell) | dilimot.russelllab.org Reviews
https://dilimot.russelllab.org
Protein Evolution Heidelberg, Prof. Rob Russell
dilimot.russelllab.org
Protein Evolution (Rob Russell)
http://www.dilimot.russelllab.org/index.shtml
A landscape of the human cilium. A landscape of the human cilium. A landscape of the human cilium. A landscape of the human cilium. Mechismo: Mechanistic interpretation of structural modifications. Mechismo: Mechanistic interpretation of structural modifications. Mechismo: Mechanistic interpretation of structural modifications. Deducing protein-protein interaction mechanism from siRNA screens. RhoA mutations in Burkitt's lymphoma. JAK3 mutations in porlymphocytic leukemia. Correlated mutaions in HIV Gag.
Services offered by Protein Evolution
http://www.dilimot.russelllab.org/services.shtml
This tool lets you interrogate data from our collaborative project on the Ciliary proteome, where we identified nearly 5000 interactions and over 50 complexes, involving more than 1000 proteins in the cilia. From Boldt, van Reeuwijk, Lu, Koutroumpas et al Nat Commun. From Betts et al, Nucl Acids Res. A database of protein-chemical interactions predicted by structure superimpositions: if you are interested in chemicals that might bind a particular protein or vice versa, then check it out. From Stark et al...
Protein Evolution (Rob Russell)
http://www.dilimot.russelllab.org/publications.shtml
An organelle-specific protein landscape identifies novel diseases and molecular mechanisms. Boldt K*, van Reeuwijk J*, Lu Q. Koutroumpas K*, Nguyen TT, Texier Y, van Beersum SEC, Horn N, Willer JR, Mans DA, Dougherty G, Lamers IJ, Coene KLM, Arts HH, Betts MJ. Roepman R* Nat Commun. Genes encoding members of the JAK-STAT pathway or epigenetic regulators are recurrently mutated in T-cell prolymphocytic leukaemia. Lopez C, Bergmann AK, Paul U, Murga-Penas EM, Nagel I, Betts MJ. Schilhabel M, Schlesner M, S...
Protein Evolution (Rob Russell)
http://www.dilimot.russelllab.org/images.shtml
Figure shows the effect knocking down components of proteins where mutations lead to 3M syndrome have on cilia in mpkCCD cells. We hypothesized that 3M Syndrome is a previously undescribed ciliary disease. Figure shows the effect of variants in patients suffereing sever ciliary diseases and how they affect specific sub-complexes and interaction within the intraflagellar transport complex B. Figure shows the architecture of the intraflagellar transport complex B deduced by our Socioaffinity metric. Figure...
Group Members in Protein Evolution
http://www.dilimot.russelllab.org/group.shtml
Protein-protein interactions, Modelling, Computational administration. Chemistry, Biochemistry, Biophysics and Molecular Biology in the lab. GTPases, Structure, Modifications. YingYing Jiang (PhD Student). Juan-Carlos Gonzales (PhD Student). Protein modifications and structure. Gurdeep Singh (MSc Student). Alumni of the Russell Group. 11/05/2016 Ciliary landscape data now available. 15/04/2015 New group member Juan-Carlos Gonzalez (PhD Student). 27/01/2015 New group member Gurdeep Singh (MSc Student).
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PepSite
http://pepsite2.russelllab.org/webservice
Run PepSite on a PDB structure. Run PepSite on your own PDB file. This PepSite web server can be accessed programmatically via a simple RESTful interface. Currently, the only implemented method is. Which queries an input peptide sequence against a protein surface identified via a PDB/chain code. Output format (see below). Web page with matches, scores, and molecular visualization. Plain text output with list of matches and scores. Match coordinates in pdb format. P-value of the best match in plain text.
PepSite
http://pepsite2.russelllab.org/examples
Run PepSite on a PDB structure. Run PepSite on your own PDB file. RNEDD4 WWIII domain from Rattus norvegicus. WW domains bind [AP]-P-P-[AP]-Y, and/or phosphoserine- phosphothreonine-containing motifs. The PDB file with id 1i5h. Is a RNEDD4 WWIII domain bound to a ENaC peptide. For more information, please refer to the Kanelis et al (2011). You run PepSite on the bound structure by specifying PDB code 1i5h. Chain W, and peptide sequence GTPPPNYDSL (see results. 74 kDa type IV collagenase from Homo sapiens.
PepSite
http://pepsite2.russelllab.org/about
Run PepSite on a PDB structure. Run PepSite on your own PDB file. PepSite was originally described in the following article:. Accurate prediction of peptide binding sites on protein surfaces. Petsalaki E, Stark A, García-Urdiales E, and Russell RB. Contributors to PepSite software development. V10 and original webserver). V2x and current webserver). Technical information about the PepSite webserver. Matches calculated with PepSite v2.2.20. Hot spots pre-calculated with PepSite v2.2.20.
Systematic discovery of peptides mediating protein interaction networks
http://lmd.russelllab.org/lmd/plos.html
These pages relate to: V. Neduva, R. Linding, I. Su-Angrand, A. Stark, F. de Massi, T.J. Gibson, J. Lewis, L. Serrano, R.B. Russell, Systematic discovery of peptides mediating protein interaction networks PLoS Biology. High confidence, pre-computed motif sets. Or if they interact with proteins sharing a common domain ( 'domain' set. And its occurence in a particular number of sequences (n) within a set of M sequences. A score which encapsulates probability of the motif and it conservation. The S. However...
PepSite
http://pepsite2.russelllab.org/help
Run PepSite on a PDB structure. Run PepSite on your own PDB file. Follow the links below to jump to the help topic of your interest. How can I use PepSite? Can I access this web server programmatically? What are the supported peptide residues? How are molecular visualizations generated? Can I provide a UniProt ID or accession instead of a PDB code? How should I cite this web server? Is PepSite merely finding cavities or conserved surfaces or both? How can I use PepSite? On the form on the left. Molecular...
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Protein Evolution (Rob Russell)
Cancer genetics meets mechanism. Cancer genetics meets mechanism. Cancer genetics meets mechanism. Genetic variants in cryptic choleostasis. Genetic variants in cryptic choleostasis. Genetic variants in cryptic choleostasis. Functional genetic variants in healthy genomes. Functional genetic variants in healthy genomes. Cancer severity from interaction mechanisms. Cancer severity from interaction mechanisms. Cancer severity from interaction mechanisms. Cancer severity from interaction mechanisms. Protein ...
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