Neighbor_Search : News, Notes, & Bugs

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Neighbor_Search has moved! We have finally installed Neighbor_Search on one of our fastest machines which has become the Structural and Computational Chemistry Group's web server machine. Neighbor_Search searches typically are completed in 10-60 seconds now! Try it - you'll like it.

News - the latest developments and enhancements.

Version 2.2 is the newest (still unofficial) version of Neighbor_Search . This version contains the latest update to the ACD inventory. The ACD inventory now uses the MFCDnnnnnnnn style of compound names compatible with the names used by MACCSII. So, once Neighbor_Search locates an ACD compound, it will tell you its MFCD name and you can go off to MACCSII with it. Conversely, if you have a MFCD compound's number from MACCSII, you can tell Neighbor_Search the MFCD number (in the place where you Add compounds to Neighbor_Search ) and he will locate the correct ACD/MFCD compound. There is a new option to edit a compound you've already input. Use the "Grins edit" button below the "Remove" button in the table which displays the List of Search Compounds. We have also corrected the bug which prevented you from using the Grins editor after inputing a SMILES string containing the # symbol, denoting a triple bond. Finally, a small convenience, we hope :) Once Neighbor_Search has accepted your input of a compound or has finished with a search, the new page display will be scrolled down a little so that the List of Search Compounds is visible at the top of the window. If you need to go to the top of Neighbor_Search , just scroll up using the scroll bar at the right, or use the PageUp button on your keyboard.

Version 2.1 is the new, official version of Neighbor_Search . This version computes properties of molecules you input, such as clogP, cmr, molecular formula, etc. Be sure to check the Properties box and then press the Redisplay button at the bottom of the List of Search Compounds display area. You must now save Preferences explicitely. This is a change to the "cookie-based" approach in v2.0. This allows you to save and use in subsequent Neighbor_Search sessions any changes you make to database selections, neighbor thresholds, print row and columns, etc.

Version 2.0 is an older version of Neighbor_Search . This version changes the layout of the compounds on the search results page so that it is easier to interpret, especially when searching for several compounds at the same time. It also corresponds more closely to the page layout as it appears when printed. There are options for customizing the number of rows and columns on the page as well as the page orientation (landscape or portrait). Any options you set will be remembered (in the browser cookie file) for your next session. This includes the similarity and neighbor threshold values, too.

Version 1.6 is an older version of Neighbor_Search . This version includes the CAP database for searching. There are now more than 600,000 total compounds available for Neighbor_Search to search! Version 1.6 has a much improved "Print Results" function which produces better looking structures than the normal Netscape print.

Version 1.5 is no longer available. This version first introduced changes to make the search significantly faster than version 1.2 and offered several new features.

Version 1.2 is an outdated version of Neighbor_Search .

Neighbor_Search requires a user's "yellow pages" username and password. The username is constructed in typical Monsanto fashion. Many users have probably forgotten their passwords, or never even knew about yellow pages in the first place (FYI, it's a unix entity). But if you use Biochem, you should have a yellow pages entry. Contact Tom Doman if you need to have your password reset.

Notes - anything that doesn't qualify as official documentation, news, bug reports, etc.

Can the ACD numbers output by Neighbor_Search be used to search the ACD in MDL products like REACCS or MACCS?

In Neighbor_Search version 2.2 and after, yes. Within MACCS this is possible using a "data search". Enter "k" to go into keyboard mode. From the "ACD Access>" prompt type "data search". A prompt will then appear saying "Enter the data field(s):". Type "1" and enter. The prompt now says "Enter the search string:". Enter the name of the desired ACD compound (such as "MFCD00087398"). When you wish to go back into graphics mode (to use the mouse for pointing & clicking) enter "g".
Searle has also licensed a standalone ACD for which a number of search and report-generation utilities have been written. Contact Tom Doman for more details.

Bugs - things that are going wrong and some workarounds.

If you are using Netscape version 1.0 (at least on the Mac) the results of Neighbor_Search calculations will not look very nice! Upgrade (at least to Netscape version 1.1) is hightly recommended.

In all versions of Neighbor_Search , there is a bug which occurs when you enter a SMILES string into the ID area and press the GRINS editor button. The bug occurs only if the SMILES contains a # character, denoting a triple bond. Once this occurs, your only option is to return to a previous page of Neighbor_Search through the use of the Netscape Back button or using the Netscape Go menu. This problem does not affect using the GRINS editor to create a molecule with a triple bond nor Neighbor_Search ability to search for, or with molecules having triple bonds.

In version2.0, a problem occurs for first-time users which causes a Netscape javaScript error box to appear. The message in the box says something about num_cols. This message box can be safely cancelled with no deleterious effects on the operation of Neighbor_Search . It simply means that Neighbor_Search could not find your previous choice for the number of columns to use for print output (since you've never used Neighbor_Search before!). This error will continue to occur, until the first time you use Neighbor_Search to generate neighbors and the Results display area appears, along with its Print Columns option. Again, this is not a fatal bug, nor will it affect the accuracy of the result of any Neighbor_Search searches.