Paper Citing NAMD - Abstract
Golden, Stephen D.; Olsen, Kenneth W.
Identification of ligand-binding pathways in truncated hemoglobins using locally enhanced sampling molecular dynamics
GLOBINS AND OTHER NITRIC OXIDE-REACTIVE PROTEINS, PART B, 437:459-475, 2008
This chapter reviews the use of a locally enhanced sampling molecular dynamics (LESMD) for the study of ligand binding in truncated hemoglobins. The method, however, can be applied to any protein-ligand system. Truncated hemoglobins appear to have a tunnel(s) potentially used by the ligand to bind. These structural features give some indication of how the ligand moves through the protein to bind but do not give the complete picture. The LESMD method has been used to investigate the pathways of ligand binding to group I truncated hemoglobins from the eubacteria Mycobacterium tuberculosis, the ciliated protozoa Paromecium caudatum, and the unicellular alga Chlamydomonas eugametos.
