A new addition to the structural bioinformatics toolbox: 3D models of short bioactive peptides from multiple sequences using feedback restrained molecular dynamics (FRMD).
Modem molecular biology techniques allow the use of new approaches for the 3D mapping of 1D information. Molecular biology techniques are capable of producing large amounts of 1D information (sequences) from a number of different sources (phage displays, ESTs, etc.). In this work, we present a technique that takes advantage of large sets of 1D information and increasingly available computer power to create 3D models. For the purpose of validation the technique is first applied to the modeling of an erythropoietin analog of known 3D structure from 1D information only. The technique is then used to model the immunoreactive region of echinococcus granulosus AgB based on phage raised mimotopes for which there is no previous structural information. The technique here presented is of general application to similar problems where 1D information is available and structure activity relationships (SAR) is needed.
Cachau
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RE
Advanced Biomedical Computing Center, National Cancer Institute-Frederick, SAIC-Frederick Inc., Frederick, Maryland 21702-1201, USA. cachau@ncifcrf.gov
González-Sapienza
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G
Burt
S K
SK
Ventura
O N
ON
D000818:Animals; D019295:Computational Biology / Q000379:methods*; D004446:Echinococcus / Q000276:immunology; D004921:Erythropoietin / Q000031:analogs & derivatives / Q000737:chemistry; D015801:Helminth Proteins / Q000737:chemistry / Q000235:genetics; D006801:Humans; D008074:Lipoproteins / Q000737:chemistry / Q000235:genetics; D010455:Peptides / Q000737:chemistry*; D017434:Protein Structure, Tertiary
D015801:Helminth Proteins; D008074:Lipoproteins; D010455:Peptides; C089273:antigen B, Echinococcus; D004921:Erythropoietin