Identification of Tunnels in Proteins, Nucleic Acids, Inorganic Materials and Molecular Ensembles.
| Authors | |
|---|---|
| Year of publication | 2006 |
| Type | Article in Periodical |
| Magazine / Source | Biotechnology Journal |
| MU Faculty or unit | |
| Citation | |
| Field | Macromolecular chemistry |
| Keywords | Tunnels; Proteins; Nucleic Acids; Inorganic Materials; Molecular Ensembles |
| Description | BACKGROUND. The main aim of this study was to develop and implement an algorithm for the rapid, accurate and automated identification of paths leading from buried protein clefts, pockets and cavities in dynamic and static protein structures to the outside solvent. RESULTS. The algorithm to perform a skeleton search was based on a reciprocal distance function grid that was developed and implemented for the CAVER program. The program identifies and visualizes routes from the interior of the protein to the bulk solvent. CAVER was primarily developed for proteins, but the algorithm is sufficiently robust to allow the analysis of any molecular system, including nucleic acids or inorganic material. Calculations can be performed using discrete structures from crystallographic analysis and NMR experiments as well as with trajectories from molecular dynamics simulations. |
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