pccompound_structure for Protein3D-(A): this filter includes compounds found in the Molecular Modeling Database (MMDB) [27].
This study considers 47,123 small molecules with experimental 3-D coordinates available from the Molecular Modeling Database (MMDB) [31] deposition in PubChem (Additional file 1).
The query return 115 different substances associated with their data sources, most of which were deposited by the Molecular Modeling Database (MMDB).
The experimental 3-D structures of small molecules were downloaded from the Molecular Modeling Database (MMDB) ligand dataset [45, 46] as available from the PubChem Substance database at the National Center for Biotechnology Information (NCBI) (as of July 1 , 2010.
The "experimental" 3-D coordinate data set of small molecules used in the present study was downloaded from the Molecular Modeling DataBase (MMDB) [21, 22] ligand dataset as available from the PubChem Substance database at NCBI on October 20, 2006.
If a PubChem substance was deposited by Molecular Modeling Database (MMDB) [43], it is most likely co-crystalized with a macromolecule (protein, RNA, or DNA) in an experimental 3-D structure.
Patch determinations with a molecular viewer of crystalline structural models downloaded from the Entrez Molecular Modeling Database Web site led to the identification of 44 DRB, 33DQB, 29 DQA, 20 DPB, and 9 DPA unique combinations of polymorphic positions.
Figure 1 shows the distributions of the non-hydrogen atom counts and the effective rotor counts (binned by whole numbers) for the experimental structures in the Molecular Modeling Database (MMDB) [21, 22] ligand dataset as downloaded from the PubChem Substance database (the MMDB contains only experimentally determined data found in the PDB).
Each histone sequence for which three-dimensional structure data is available is linked to the corresponding entry in both PDB and the Molecular Modeling Database (MMDB) (35).
A large subset of BIND consists of a set of protein small molecule interactions that were computationally extracted from 3D protein structures from the Molecular Modeling Database (MMDB), originally from the Protein Data Bank (PDB) (20).
