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The ConSurf Server | consurf.tau.ac.il Reviews
https://consurf.tau.ac.il
You are using a web browser that we do not support. Our website will not work properly. Please update to a newer version or download a new web browser, such as Chrome or Firefox. Server for the Identification of Functional Regions in Proteins. Analyze Nucleotides or Amino Acids? Please note: An improved HMMER search for homologous proteins has been added, and suggested as default. Questions and comments are welcome!
consurf.tau.ac.il
The ConSurf Server
http://consurf.tau.ac.il/faq.php
Server for the Identification of Functional Regions in Proteins. ConSurf Frequently Asked Questions (FAQ). 1 What is the minimum number of sequences required to get reliable results? 2 What if I get only few homologous sequences for my query protein? 3 What are the advantages of using phylogenetic tree? 4 Should I use the Bayesian or the Maximum Likelihood method? 5 Is it possible for the extreme grades 1 and 9 to be unoccupied? Which conditions give this result? 7 How can I produce a ConSurf picture?
The ConSurf Server
http://consurf.tau.ac.il/Old_Versions.php
Server for the Identification of Functional Regions in Proteins. ConSurf Ver. 3.0. ConSeq Ver 1.1.
The ConSurf Server
http://consurf.tau.ac.il/gallery.php
Server for the Identification of Functional Regions in Proteins. Click on the linked example titles to view ConSurf results and the rotatable molecules colored according to ConSurf conservations scores, or click on the static figures to see them in greater detail. Color coding scheme of ConSurf. Example 1: MHC Class I Heavy Chain. H-2Kb, PDB ID 2VAA chain A). Complexed With Beta-2 Microglobulin (Chain B) and Vesicular Stomatitis Virus Nucleoprotein (fragment 52-59, chain P). Example 2: Potassium Channel.
The ConSurf Server
http://consurf.tau.ac.il/credits.php
Server for the Identification of Functional Regions in Proteins. Citing ConSurf and ConSurf Credits. In citing the ConSurf server please refer to. Celniker G., Nimrod G., Ashkenazy H., Glaser F., Martz E., Mayrose I., Pupko T., and Ben-Tal N. 2013. ConSurf: Using Evolutionary Data to Raise Testable Hypotheses about Protein Function. 2013 March 10, doi: 10.1002/ijch.201200096 [ABS]. Ashkenazy H., Erez E., Martz E., Pupko T. and Ben-Tal N. 2010. 2010; DOI: 10.1093/nar/gkq399; PMID: 20478830 [ABS]. Comparis...
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Useful Tools
http://www.nysgrc.org/psi3/tools.html
Disorder prediction : DISOPRED,. Sequence searches : BLAST,. Signal peptide prediction : PHOBIUS. Crystallizability prediction: Xtalpred,. Database of comparative protein structure models : ModBase. Comparative modeling web-server : ModWeb. Comparative Modelling using multiple templates : M4T. Multiple Mapping Method : MMM. Homology detection by HMM-HMM comparison : HHPRED. Protein Structure Prediction : mGenTHREADER. Integrated Construct Design Interface: ICDI. Protein Structure Prediction : PSIPRED.
ConSurf-DB | Evolutionary conservation profiles of proteins
http://bental.tau.ac.il/new_ConSurfDB
Last update: January 17th, 2013 on a set of 80,479 protein structures. ConSurf-DB differs from ConSurf. In that ConSurf-DB provides pre-calculated conservation profiles, while ConSurf enables considerable flexibility in setting the parameters of the calculation, and accepts optional uploads of atomic coordinates, multiple sequence alignments, and phylogenetic trees for use in the calculation. Enter the PDB ID. If you don't know the PDB ID, please enter the protein sequence here:.
ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids
http://nar.oxfordjournals.org/cgi/content/abstract/gkq399
View Current Issue (Volume 44 Issue 14 19 August 2016). ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Department of Cell Research and Immunology,. Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel and. Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA. To whom correspondence should be addressed. Tel: 972 3 640 6709. March 8, 2010.
Resources
http://doxey.uwaterloo.ca/resources.html
Applied Bioinformatics Research Group. Dept of Biology, UWaterloo. Doxey Lab Google Group. Homolog detection and sequence alignment. R package), Figtree. Genome Browsing and Analysis. Genome Browser, Galaxy. Haplotype Analysis and Visualization.
Schepartz Laboratory | Cool Links
http://www.schepartzlab.yale.edu/links.html
Genomics and Proteomics Tools. ISI The Web of Knowledge. Yale University Medical School online journals. 8211; an interactive source of information about the elements. 8211; a toolbox for synthetic chemistry. 8211; search for commercial compounds with a particular substructure. 8211; chemical structures of pharmacological agents. 8211; statistical tools. IDT SciTools - A suite of tools to help with design and analysis of oligonucleotides. A guide to commercial antibody suppliers. 8211; PCR primer design.
Florencio Pazos. Xdet - MTreedet
http://csbg.cnb.csic.es/pazos/Xdet
Implements two methods for detecting residues responsible for functional especificity in multiple sequence alignments. These kind of positions, presenting a family-dependent (or function-dependent) conservation pattern, complement the fully-conserved positions as predictors of functionality. They are usually related to functional specificity. The first method is the "mutational behaviour (MB) method", previously implemented in the MTreedet. Is freely available for academic users. Other users, please ...
Databases & Bioinformatic Tools | Amit Kessel Ph.D
https://amit1b.wordpress.com/databases-bioinformatic-tools
The Molecules of Life. Amit Kessel Ph.D. 124; Comments RSS. The Molecules of Life. Proteins: Nature’s Nano-Machines. Amino Acids: Chemistry, Biochemistry & Nutrition. Antimicrobial Peptides: A Molecular Weapon against Bacteria. Biochemistry and Molecular Biology Animations. Online Exams and Glossaries of Biochemistry and Cell Biology. The Living Cell Gallery. Computational Methods and Tools in Biophysics. Databases and Bioinformatic Tools. Databases and Bioinformatic Tools. 1 Protein and Enzyme Databases.
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Domingo, 5 de diciembre de 2010. Maybe this kind of thing should be teaching in school frequently and not just for being a popular thing just because is important to know this stuff, is our world and we need to take care of. Enviar por correo electrónico. Enviar por correo electrónico. Jueves, 14 de octubre de 2010. The miners story was so terrible, there’s no doubt about that! People from all the world was follow the story, but what’s gonna happend now? But what is gonna happend now? My wishes for the m...
The ConSurf Server
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ConSurf Test Server
Server for the Identification of Functional Regions in Proteins. Analyze Nucleotides or Amino Acids? Visitors Since June 23, 2002. Questions and comments are welcome!
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