Biomedical Engineering Reference
In-Depth Information
structure that can be rotated in 3D space using a visualization program such as RasMol, Chimera, or
SWISS-PDBViewer. Data are typically subject to numerical analysis as well as visualization, in order
to provide a quantitative measure of accuracy and to determine whether the underlying model needs
to be improved upon.
Documentation, although not represented as a formal step in
Figure 9-4
, is key to model validation,
reuse, and communication with others. For example, the data format used by many molecular
modeling systems follows the PDB format, which includes extensive documentation with each
molecule described in the database. The partial listing of structure 1A3N from the PDB, shown in
Figure 9-5
, documents the geometry and stereochemistry of the Deoxy Human Hemoglobin molecule.
Figure 9-5 Documentation of Data. Data documentation in the PDB is in the
form of header data in each description of protein structure. This example,
taken from Deoxy Human Hemoglobin (PDB ID 1A3N), describes factors
relating to geometry and stereochemistry of the data described in the main
body of the file.
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 NZ LYS B 66 - O HOH 394 0.958
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 4*RMSD AND BY MORE THAN 0.150 ANGSTROMS (M=MODEL
REMARK 500 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 500 NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991
REMARK 500
REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION
REMARK 500
REMARK 500 0 LYS A 60 CG LYS A 60 CD 0.621
REMARK 500 0 LYS A 90 CG LYS A 90 CD 0.231
