This page lists all of the groupings for the database of morphs. The annotations are divided into several classes, and may be curated manually or automatically (or even both). Clicking on the title for each set will generate a list of morphs in that category.

The sets vary in size from a handful to thousands; not all are intended for general use but we have described all here for clarity.

Major groupings

User-submitted morphs: These have been manually created by web form submission or by the admins. Continuously updated, annotated as regularly as time allows.

Automated set 1: An early attempt at a PDB-wide structure comparison. See article by Krebs et al. (2001) in Proteins for details on creation and composition.

Automated set 2: A second run of PDB-wide structure comparisons using a different method. See article by Alexandrov et al. (2005) in Protein Science.

All automated morphs: Both of the above sets. They are both highly redundant and poorly curated; both are static and no longer annotated.

Representative morphs: The best example of a motion, manually curated. Only a few (and usually just one) exist for each motion.

Morphs associated with motions: All morphs of proteins contained in the Motions database. This set is often highly redundant, but also more diverse.

Morphs without motions: These morphs either haven't been linked up with their corresponding motion, or no motion exists for this protein. Sometimes this is simply administrative oversight, and we periodically check this set for both old and new motions. However, many cases exist in which the morph is not appropriate for a motion, e.g. the structures are not actually significantly different enough to meet our criteria for inclusion. There are also a smaller number for which we haven't yet determined which structures were morphed, due to "anonymous" PDB files being uploaded.

PDB ID(s) known: All morphs for which one or more PDB IDs was specified. (More of a filter for our purposes than anything.)




Structure type

RNA structures: A more recent set consisting entirely of RNA motions morphed using one of the newer servers. May include proteins, but so far most are RNA-only. Since there are far fewer RNA structures this set is not very well-developed, but there are several significant motions.

Protein Kinases: A manually curated set of protein kinase morphs. Conformational changes in this family have been extensively studied, and although the motions are similar they vary widely in the details. See for example review by Huse and Kuriyan (2002).

Alpha-helical proteins: Derived from Automated set 2, annotated by CATH classification of input structures. Includes only all-alpha proteins.

Beta-sheet proteins: Derived from Automated set 2, annotated by CATH classification of input structures. Includes only all-beta proteins.

Mixed alpha/beta proteins: Derived from Automated set 2, annotated by CATH classification of input structures. Includes only proteins that contain both alpha helices and beta sheets.

Rossman-fold proteins: Derived from Automated set 2, annotated by CATH classification of input structures. Includes any protein that contains a Rossman fold; by definition, this is a subset of the mixed alpha/beta grouping.

Hinged domain motions: The most common type of motion in the database. This set includes any morph linked to a motion in this family.




Annotations

Top 10% RMSD: User-submitted morphs with high overall Calpha RMSD values between initial and final structures.

Top 10% translation: User-submitted morphs with a high value for the translation statistic (see Krebs and Gerstein 2000).

Top 10% maximum atom deviation: User submitted morphs with a large change in position for any atom, with one core aligned.

Catalytic site atlas: For these morphs, the morphs page has a button to highlight the active site residues, according to the Catalytic Site Atlas. This feature is briefly described in Flores, Echols, et al. (2006).

Catalytic site atlas (non-redundant): A nonredundant subset of the Catalytic Site Atlas morphs.

Nonredundant: A nonredunant subset of all the morphs in molmovdb, compiled by homology to nrdb90. This will be described in our upcoming Hinge Survey paper.

Hinge Atlas: A set of morphs for which hinges have been manually selected. The morph page has a button to highlight the hinge residues. This set is useful for studies of protein flexibility. We describe its use in benchmarking our FlexOracle hinge predictor in an upcoming paper by Flores et al.
Download a pre-generated mysqldump file of this set here, or generate a new mysqldump file here.
Alternatively, download a pre-generated tab-delimited text file of this annotation here, or regenerate it here.
Download a pre-generated tarball (.tgz) of the set data here. When unzipped this will create 215 directories, each named with the corresponding morph ID. Each directory will contain files named ff0.pdb to ff[MAX].pdb, the structure files for the corresponding morph movie.

Hinge Atlas Gold: This is a small set of morphs especially selected for benchmarking structure based hinge predictors, although it could be useful for other flexibility studies as well. All of the proteins in this set meet the following criteria: 1. The biological molecule consists of a single chain. 2. They are crystallized with small or no ligand. 3. The two structures in a morph pair are represent a biologically relevant domain motion. The morph page has a button to highlight the annotated hinge residues. We describe its use in benchmarking FlexOracle, StoneHinge, NSHP, and TLSMD in an upcoming paper by Flores, Keating et al.
Download a pre-generated mysqldump file of this set here, or generate a new mysqldump file here.
Alternatively, download a pre-generated tab-delimited text file of this annotation here, or regenerate it here. Download a pre-generated tarball (.tgz) of the set data here. When unzipped this will create 20 directories, each named with the corresponding morph ID. Each directory will contain files named ff0.pdb to ff[MAX].pdb, the structure files for the corresponding morph movie.

Fragment Hinge Motions: A set of morphs with hinge bending motions involving fragments smaller than domains. Hinges locations are annotated as for the Hinge Atlas.

FlexProt Hinges: A set of morphs for which hinges have been annotated by computer. We used Shatsky and Wolfson's FlexProt program to identify the hinges. This set is less useful than the Hinge Atlas set.




FlexOracle morphs

Featured FlexOracle set: Set of single-chain, biological molecules used to benchmark FlexOracle in our upcoming paper.

FlexOracle (implicit solvent): Morphs with implicit solvent hinge predictions.

FlexOracle (explicit solvent): Morphs with explicit solvent hinge predictions.

FlexOracle implicit + explicit: Morphs with both implicit and explicit solvent hinge predictions.





Last modified 12-30-05 by Nat Echols