services.mbi.ucla.edu

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Mdash; Laboratory Services. Welcome to the home of web services provided by the Molecular Biology Institute. At the University of California, Los Angeles. Chemical Similarity Network Analysis Pull-down (CSNAP). A web server for drug targets prediction based on chemical similarity networks. Perform Ellipsoidal Truncation and Anisotropic Scaling. Diffusion accessibility gives a measure of surface accessibility that is longer range in nature than ordinary solvent accessibility. Self Rotation Function Server.

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Mdash; Laboratory Services. Welcome to the home of web services provided by the Molecular Biology Institute. At the University of California, Los Angeles. Chemical Similarity Network Analysis Pull-down (CSNAP). A web server for drug targets prediction based on chemical similarity networks. Perform Ellipsoidal Truncation and Anisotropic Scaling. Diffusion accessibility gives a measure of surface accessibility that is longer range in nature than ordinary solvent accessibility. Self Rotation Function Server.

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1 ucla doe lab

2 available servers

3 diffraction anisotropy server

4 diffusion accessibility server

5 x dval

6 zipperdb

7 more services here

8 questions

9 contact tom holton

10 coupons

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Laboratory Services | services.mbi.ucla.edu Reviews

https://services.mbi.ucla.edu

Mdash; Laboratory Services. Welcome to the home of web services provided by the Molecular Biology Institute. At the University of California, Los Angeles. Chemical Similarity Network Analysis Pull-down (CSNAP). A web server for drug targets prediction based on chemical similarity networks. Perform Ellipsoidal Truncation and Anisotropic Scaling. Diffusion accessibility gives a measure of surface accessibility that is longer range in nature than ordinary solvent accessibility. Self Rotation Function Server.

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services.mbi.ucla.edu

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index

http://services.mbi.ucla.edu/CSNAP

A network-based approach for automated compound target identification. CSNAP web server (version 1.0): start here. The server is freely accessible without any log-in requirement. The website has been tested and optimized for Firefox, Opera, Chrome and Safari. Please see Q&A page for additional details. This material is based upon work supported by the National Science Foundation under Grant Number MCB1243645.

2

Diffusion Accessibility

http://services.mbi.ucla.edu/DiffAcc

Mdash; Diffusion Accessibility. Click on "Do Calculation". There you will upload a PDB file and retrieve a modified version with the required information in the temperature factor column. Click on "Get Coloring Script" to download the PyMol script. You need only do this once, not each time you analyze a new PDB file. Information about running the script is located at that link. An example of the program applied to the MHC peptide binding domain is shown.

3

Disulfide Bond Dihedral Angle Energy Server

http://services.mbi.ucla.edu/disulfide

Disulfide Bond Dihedral Angle Energy Server. 1986 ; 261(33):15480-5.]. The Dihedral Energy, and dihedral angles from the uploaded are compared to disulfides found in a large non-redundant set of structures from the Protein Data Bank. Model Disulfide Showing Five Dihedral Angles. Please upload a PDB coordinate. Questions or comments on the Disulfide Bond Server may be sent to: Marcin Apostol.

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SAVES

http://services.mbi.ucla.edu/SAVES

PdbSNAFU (Check for ADIT compliance). This metaserver runs 6 programs for checking and validating protein structures during and after model refinement. This server processed 2,962.9 jobs per month in the last 12 months. See more usage statistics here. Checks the stereochemical quality of a protein structure by analyzing residue-by-residue geometry and overall structure geometry. [ Reference. Calculates the volumes of atoms in macromolecules using an algorithm which treats the atoms like hard spheres and ...

5

CrowdPhase - An online game for solving the phase problem.

http://services.mbi.ucla.edu/crowdphase

CrowdPhase. An online game for solving the phase problem. Welcome to the beta version of CrowdPhase! Crowdphase is an online multiplayer game for solving the phase problem in X-ray crystallography. X-ray crystallography is a method based on X-ray diffraction for determining the molecular structure of materials that can form crystals. In biology, this can be used to solve the structure of molecules such as proteins, DNA or drugs. 1 Create an account. Already have an account? 2 Join a game. J Jorda, M....

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proknow.mbi.ucla.edu

ProKnow: Batch Submission

http://proknow.mbi.ucla.edu/proknow/batch_submit

Molecular Biology Institure at the University of California, Los Angeles.

proknow.mbi.ucla.edu

ProKnow: Helpful Tips

http://proknow.mbi.ucla.edu/proknow/tips

Scenario 1. You have known structure but unknown function. Scenario 2. You have known structure and unknown function and novel fold. Scenario 3. You have known structure and known function, but suspect that your protein does something more. Scenario 4. You have unknown structure and unknown function, and have some information on the domain boundaries. Scenario 5. You have unknown structure and unknown function, and no other information. Check the "Click here to get a description of your clues" and see wh...

proknow.mbi.ucla.edu

ProKnow: Help Page

http://proknow.mbi.ucla.edu/proknow/help

Please read the submission information by clicking the relevant links in the submission page. In particular, read the " Tips. And " Known Problems. Link To know how ProKnow works you may read the paper mentioned below, or look at the poster. Pal D and Eisenberg D. (2005). Inference of protein function from protein structure. Structure 13, 121-130. PDF. Molecular Biology Institure at the University of California, Los Angeles.

proknow.mbi.ucla.edu

ProKnow: The FSSP File

http://proknow.mbi.ucla.edu/proknow/fssp_files_help

The FSSP file is an output from the DALI program. For every PDB file submitted to the ProKnow program, at least one FSSP file is needed. If the PDB file has multiple domains, FSSP file for each domain need to be submitted. Please submit your PDB file to the DALI Server and use the files obtained (the FSSP files) for input into the ProKnow program. An example FSSP file (old format). An example FSSP file (new format). Molecular Biology Institure at the University of California, Los Angeles.

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services.mbi.ucla.edu

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Mdash; Laboratory Services. Welcome to the home of web services provided by the Molecular Biology Institute. At the University of California, Los Angeles. Chemical Similarity Network Analysis Pull-down (CSNAP). A web server for drug targets prediction based on chemical similarity networks. Perform Ellipsoidal Truncation and Anisotropic Scaling. Diffusion accessibility gives a measure of surface accessibility that is longer range in nature than ordinary solvent accessibility. Self Rotation Function Server.

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