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revision 1.48, Tue Apr 10 06:13:54 2007 UTC revision 1.49, Fri May 11 06:37:38 2007 UTC
# Line 466  Line 466 
466                  </Field>                  </Field>
467              </Fields>              </Fields>
468          </Entity>          </Entity>
469            <Entity name="PDB" keyType="id-string">
470                <Notes>A PDB is a protein database containing information that can be used to determine
471                the shape of the protein and the energies required to dock with it. The ID is the
472                four-character name used on the PDB web site.</Notes>
473                <Fields>
474                    <Field name="docking-count" type="int">
475                        <Notes>The number of ligands that have been docked against this PDB.</Notes>
476                    </Field>
477                </Fields>
478                <Indexes>
479                    <Index>
480                        <IndexFields>
481                            <IndexField name="docking-count" order="descending" />
482                            <IndexField name="id" order="ascending" />
483                        </IndexFields>
484                    </Index>
485                </Indexes>
486            </Entity>
487            <Entity name="Ligand" keyType="id-string">
488                <Notes>A Ligand is a chemical of interest in computing docking energies against a PDB.
489                The ID of the ligand is an 8-digit ZINC ID number.</Notes>
490                <Fields>
491                    <Field name="name" type="long-string">
492                        <Notes>Chemical name of this ligand.</Notes>
493                    </Field>
494                </Fields>
495            </Entity>
496      </Entities>      </Entities>
497      <Relationships>      <Relationships>
498            <Relationship name="IsProteinForFeature" from="PDB" to="Feature" arity="MM">
499                <Notes>Relates a PDB to features that produce highly similar proteins.</Notes>
500                <Fields>
501                    <Field name="score" type="float">
502                        <Notes>Similarity score for the comparison between the feature and
503                        the PDB protein. A lower score indicates a better match.</Notes>
504                    </Field>
505                    <Field name="start-location" type="int">
506                        <Notes>Starting location within the feature of the matching region.</Notes>
507                    </Field>
508                    <Field name="end-location" type="int">
509                        <Notes>Ending location within the feature of the matching region.</Notes>
510                    </Field>
511                </Fields>
512                <ToIndex>
513                    <Notes>This index enables the application to view the PDBs of a
514                    feature in order from the closest match to the furthest.</Notes>
515                    <IndexFields>
516                        <IndexField name="score" order="ascending" />
517                    </IndexFields>
518                </ToIndex>
519                <FromIndex>
520                    <Notes>This index enables the application to view the features of
521                    a PDB in order from the closest match to the furthest.</Notes>
522                    <IndexFields>
523                        <IndexField name="score" order="ascending" />
524                    </IndexFields>
525                </FromIndex>
526            </Relationship>
527            <Relationship name="DocksWith" from="PDB" to="Ligand" arity="MM">
528                <Notes>Indicates that a docking result exists between a PDB and a ligand. The
529                docking result describes the energy required for the ligand to dock with
530                the protein described by the PDB. A lower energy indicates the ligand has a
531                good chance of disabling the protein. At the current time, only the best
532                docking results are kept.</Notes>
533                <Fields>
534                    <Field name="reason" type="id-string">
535                        <Notes>Indication of the reason for determining the docking result.
536                        A value of [b]Random[/b] indicates the docking was attempted as a part
537                        of a random survey used to determine the docking characteristics of the
538                        PDB. A value of [b]Rich[/b] indicates the docking was attempted because
539                        a low-energy docking result was predicted for the ligand with respect
540                        to the PDB.</Notes>
541                    </Field>
542                    <Field name="tool" type="id-string">
543                        <Notes>Name of the tool used to produce the docking result.</Notes>
544                    </Field>
545                    <Field name="total-energy" type="float">
546                        <Notes>Total energy required for the ligand to dock with the PDB
547                        protein, in kcal/mol. A negative value means energy is released.</Notes>
548                    </Field>
549                    <Field name="vanderwalls-energy" type="float">
550                        <Notes>Docking energy in kcal/mol that results from the geometric fit
551                        (Van der Waals force) between the PDB and the ligand.</Notes>
552                    </Field>
553                    <Field name="electrostatic-energy" type="float">
554                        <Notes>Docking energy in kcal/mol that results from the movement of
555                        electrons (electrostatic force) between the PDB and the ligan.</Notes>
556                    </Field>
557                </Fields>
558                <FromIndex>
559                    <Notes>This index enables the application to view a PDB's docking results from
560                    the lowest energy (best docking) to highest energy (worst docking).</Notes>
561                    <IndexFields>
562                        <IndexField name="total-energy" order="ascending" />
563                    </IndexFields>
564                </FromIndex>
565                <ToIndex>
566                    <Notes>This index enables the application to view a ligand's docking results from
567                    the lowest energy (best docking) to highest energy (worst docking). Note that
568                    since we only keep the best docking results for a PDB, this index is not likely
569                    to provide useful results.</Notes>
570                </ToIndex>
571            </Relationship>
572          <Relationship name="IsFamilyForFeature" from="Family" to="Feature" arity="MM">          <Relationship name="IsFamilyForFeature" from="Family" to="Feature" arity="MM">
573              <Notes>This relationship connects a protein family to all of its PEGs and connects              <Notes>This relationship connects a protein family to all of its PEGs and connects
574              each PEG to all of its protein families.</Notes>              each PEG to all of its protein families.</Notes>

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