Sampling-Based Motion Planning for Tracking Evolution of Dynamic Tunnels in Molecular Dynamics Simulations

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68407700%3A21230%2F19%3A00326510" target="_blank" >RIV/68407700:21230/19:00326510 - isvavai.cz</a>

Alternative codes found

RIV/00216224:14330/19:00107165

Result on the web

<a href="https://doi.org/10.1007/s10846-018-0877-6" target="_blank" >https://doi.org/10.1007/s10846-018-0877-6</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1007/s10846-018-0877-6" target="_blank" >10.1007/s10846-018-0877-6</a>

Result language

angličtina

Original language name

Sampling-Based Motion Planning for Tracking Evolution of Dynamic Tunnels in Molecular Dynamics Simulations

Original language description

Proteins are involved in many biochemical processes. The behavior of proteins is highly influenced by the presence of internal void space, in literature denoted as tunnels or cavities. Tunnels are paths leading from an inner protein active site to its surface. The knowledge about tunnels and their evolution over time, captured in molecular dynamics simulations, provides an insight into important protein properties (e.g., their stability or activity). For each individual snapshot of molecular dynamics, tunnels can be detected using Voronoi diagrams and then aggregated over time to trace their behavior. However, this approach is suitable only when a given tunnel is detected in all snapshots of molecular dynamics. This is often not the case of traditionally used approaches to tunnel computation. When a tunnel becomes too narrow in a particular snapshot, the existing approaches cannot detect this case and the tunnel completely disappears from the results. On the other hand, this situation can be quite common as tunnels move, disappear and appear again, split, or merge. Therefore, in this paper we propose a method which enables to trace also tunnels in those missing snapshots. We call them dynamic tunnels and we use the sampling-based motion planning to compute them. The Rapidly Exploring Random Tree (RRT) algorithm is used to explore the void space in each frame of the protein dynamics. The void space is represented by a tree structure that is transferred to the next frame of the dynamics and updated to remove collisions and to cover newly emerged free regions of the void space. If the void space reaches the surface of the protein, a dynamic tunnel is reconstructed by tracking back in the tree towards a desired place (i.e., the active site).

Czech name

—

Czech description

—

Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Project

<a href="/en/project/GA17-07690S" target="_blank" >GA17-07690S: Methods of Identification and Visualization of Tunnels for Flexible Ligands in Dynamic Proteins</a><br>

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2019

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Journal of Intelligent and Robotic Systems

ISSN

0921-0296

e-ISSN

1573-0409

Volume of the periodical

93

Issue of the periodical within the volume

3-4

Country of publishing house

NL - THE KINGDOM OF THE NETHERLANDS

Number of pages

23

Pages from-to

763-785

UT code for WoS article

000459439400024

EID of the result in the Scopus database

2-s2.0-85048538078