14 Matching Annotations
  1. Mar 2017
    1. Options Identical Structures Similar Compounds, score >= 95% Similar Compounds, score >= 90% Similar Compounds, score >= 80% Identical Structures Similar Structures with  same connectivity any tautomer same stereoisomer same isotopical labels same stereochemistry and isotopes non-conflicting stereochemistry same isotopes and non-conflicting stereoisomers   threshold >=  99% 98% 97% 96% 95% 93% 90% 85% 80% 70% 60%   Substructure Superstructure Substructure Superstructure match stereochemistry  Ignore Exact Relative Nonconflicting  and  Match isotopes Match charges Match tautomers Ringsystems not embedded Single/double bonds match aromatic bonds Chain bonds match ring bonds Strip hydrogen   Molecular Formula with  exact stoichiometry allow other element   Sort results by: Shape-then-featureFeature-then-shapeShape-and-featureConformer Id Output to: PubChem 3D Alignment ViewerNCBI EntrezTable Summary Time Limit(seconds):  unlimited 30 60 90 300 600 3,600      Result Limit: 10 50 100 500 1,000 10,000 100,000 2,000,000  
    1. PubChem Substructure FingerprintV1.3 http://pubchem.ncbi.nlm.nih.govPage 4 of 21 5/1/2009 7:21:06 AM PubChem Substructure Fingerprint Description (cont.)

      In studying PubChem Substructure Fingerprint, do we need to know all the Bit position and Bit substructure for further use? (Daniel)

    1. Tanimoto coefficient6-8

      I'm trying to understand how to use the Tanimoto coefficient. I don't see any example to reference to. (Daniel)

    2. However, molecular formula search implemented in some databases, including PubChem Chemical Structure Search, has an option to allow other elements in returned hits (e.g., C6H6O or C6H6N2O for the “C6H6” query).

      Why is it has option to allow other elementsin returned hits when we type C6H6 or any other related molecules? Amita

    3. The most common types of molecular fingerprints are structural keys, which encode structural information of a molecule into a binary string (that is, a string of 0’s and 1’s).  The position of each number in this string corresponds to a particular fragment.  If the molecule has a particular fragment, the corresponding bit position is set to 1, and otherwise to 0.  Note that there are many different ways to design molecular fingerprints, depending on what fragments are included in the fingerprint definition.  PubChem uses its own fingerprint called PubChem subgraph fingerprints.

      I am confused with binary string and fingerprint. How does it work to recognize molecules? Amita

    4. PubChem provides two web-based tools that allow users to perform a cluster analysis of PubChem data:  the Structure Clustering tool and Structure-Activity Relationship (SAR) Analysis tool.

      I am confused using structure clustering tool, how can we use this? I practised to use this tool but I did not get any results. Amita

    5. The Structure-Activity Relationship (SAR) Analysis tool

      Confusion on using this tool. Amita

    6. On the contrary, superstructure search returns molecules that comprise or make up the provided chemical structure query (that is, substructures that is contained in the query superstructure).  It should be noted that substructure search does not give you substructures of the query and that superstructure search does not return superstructures of the query.

      How do we know which one is substructure and superstructure? Amita

    1. Search resultsItems: 1 to 20 of 1545467

      I did a SMILES query under the substructure and superstructure search for [CH2][CH2][OH] and i got this results. From what i read it is not what i was expecting. (Daniel)

    1. ELISA

      The PubChem BioAssay Classification Tree is really an amazing feature. Within a few minutes I was able to go through the classification of bacteria to a species I use to work with in microbiology, combine the sources with a few keywords and find the exact AID needed to run confirmation tests. This being coupled to the Pubmed side on the publication is a great feature for scientists to have access to.


      I have been using the beta testing database to try and search for some compounds. In PubChem homepage, it comes up fine but not here. Is it because it is still in the testing phase? (Daniel)

    1. The method is also used to quantify the degree of chirality of asymmetric molecules and to investigate the chirality of biphenyl and the amino acids.

      This article was cited in the OLCC Cheminformatics Class Module 6 for atom-centered Gaussian-shape comparison method. I will see if i can access the full article from campus tomorrow, but its very difficult for me to understand how causing a gaussian adaptation to a molecule would help to provide information about the degree of chirality on certain molecules. for example, it would be difficult to understand the shape of a miniature model sailboat inside of a glass bottle if the only shape you see is the outer bottle and not whats contained inside.


    1. ROCS is a fast shape comparison application, based on the idea that molecules have similar shape if their volumes overlay well and any volume mismatch is a measure of dissimilarity. It uses a smooth Gaussian function to represent the molecular volume [5], so it is possible to routinely minimize to the best global match.

      I assume that the ROCS description here that talks about volume overlays is what is mentioned on the olcc module 6 page about finding the best alignmentfor a 3D structure overlay. it seems that through the gaussian blur around the chemical being matched against others that many of the individual bonds would not be compared in the matching process.


    1. The method provides good accuracy across a range of organic and drug-like molecules. The core parameterization was provided by high-quality quantum calculations, rather than experimental data, across ~500 test molecular systems. The method includes parameters for a wide range of atom types including the following common organic elements: C, H, N, O, F, Si, P, S, Cl, Br, and I. It also supports the following common ions: Fe+2, Fe+3, F-, Cl-, Br-, Li+, Na+, K+, Zn+2, Ca+2, Cu+1, Cu+2, and Mg+2. The Open Babel implementation should automatically perform atom typing and recognize these elements.