pfp.technion.ac.il

Patch Finder Plus

A new and upgraded server is available: BindUP. Including all PatchFinderPlus features and many more. We highly recommend using it instead of PatchFinderPlus. Enter a PDB ID:. Or, upload a PDB file:. Calculate all protein chains (each chain is calculated separately). Or, select a protein chain identifier:. Send a link to the results by E-mail. E-mail address:. Note: the electrostatic patches on the protein are visualized using Jmol viewer. To download the latest version of Java.

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Patch Finder Plus | pfp.technion.ac.il Reviews

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A new and upgraded server is available: BindUP. Including all PatchFinderPlus features and many more. We highly recommend using it instead of PatchFinderPlus. Enter a PDB ID:. Or, upload a PDB file:. Calculate all protein chains (each chain is calculated separately). Or, select a protein chain identifier:. Send a link to the results by E-mail. E-mail address:. Note: the electrostatic patches on the protein are visualized using Jmol viewer. To download the latest version of Java.

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3 versions

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6 chain selection

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Patch Finder Plus | pfp.technion.ac.il Reviews

https://pfp.technion.ac.il

A new and upgraded server is available: BindUP. Including all PatchFinderPlus features and many more. We highly recommend using it instead of PatchFinderPlus. Enter a PDB ID:. Or, upload a PDB file:. Calculate all protein chains (each chain is calculated separately). Or, select a protein chain identifier:. Send a link to the results by E-mail. E-mail address:. Note: the electrostatic patches on the protein are visualized using Jmol viewer. To download the latest version of Java.

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pfp.technion.ac.il

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Patch Finder Plus

http://pfp.technion.ac.il/versions.html

Jmol was upgraded to the latest version (Jmol-14.0.11). This version is compatible with the most updated security requirements of Java. What is new in version 2.2? The electrostatic potential calculation is now conducted by the APBS. Software. The grid size is now dynamically set for each protein chain and there is no limitation of the protein chain size. The Patch Finder algorithm was improved in terms of accuracy and efficiency. What is new in version 2.0? Grid spacing was changed to 1Å. Shula Shazman,...

2

Patch Finder Plus

http://pfp.technion.ac.il/overview.html

Patch Finder Plus is an automatic server to extract and display the largest positive electrostatic patch on a protein surface. The algorithm automatically assigns surface positive patches by looking for adjacent points on the protein surface that meet a given electrostatic potential cutoff. In the current version of Patch Finder Plus, the potential cutoff is fixed to 2 kT/e. The algorithm is built of five major steps:. Choosing the largest positive patch for each protein chain.

3

Patch Finder Plus

http://pfp.technion.ac.il/manual.html

Patch Finder Plus Manual. Patch Finder Plus requires a coordinate file in PDB format. The input can be given in one of two ways:. Supply a valid PDB ID. A 4 character alphanumeric identifier). In this case Patch Finder will download the file from RCSB PDB. Upload a user-defined coordinate file. Of a known structure or a model) in PDB format. An example of Patch Finder Plus output file:. Patch Finder Plus visualizes the largest positive patch on the protein surface using Jmol viewer. A list of the residue...

4

Patch Finder Plus

http://pfp.technion.ac.il/index.html

A new and upgraded server is available: BindUP. Including all PatchFinderPlus features and many more. We highly recommend using it instead of PatchFinderPlus. Enter a PDB ID:. Or, upload a PDB file:. Calculate all protein chains (each chain is calculated separately). Or, select a protein chain identifier:. Send a link to the results by E-mail. E-mail address:. Note: the electrostatic patches on the protein are visualized using Jmol viewer. To download the latest version of Java.

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Mandel-Gutfreund Lab | Tools

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RBPmap: a web server for mapping binding sites of RNA-binding proteins. Paz et al., Nucleic Acids Res., 2014. DRIMust: a web server for Discovering Rank Imbalanced Motifs Using Suffix Trees. Leibovich et al., Nucleic Acids Res., 2013. SFmap: a web server for motif analysis and prediction of splicing factor binding sites. Paz et al., Nucleic Acids Res., 2010. NAbind: classifying NA-binding proteins based on electrostatic properties. Shazman et al., PLoS CB., 2008.

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pfp.technion.ac.il

Patch Finder Plus

A new and upgraded server is available: BindUP. Including all PatchFinderPlus features and many more. We highly recommend using it instead of PatchFinderPlus. Enter a PDB ID:. Or, upload a PDB file:. Calculate all protein chains (each chain is calculated separately). Or, select a protein chain identifier:. Send a link to the results by E-mail. E-mail address:. Note: the electrostatic patches on the protein are visualized using Jmol viewer. To download the latest version of Java.

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