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This is the third webinar in BioExcel’s webinar series on computational methods and applications for biomolecular research. The series cover broad topics related to the latest development of major software packages; their application to modelling and simulation; best practices for performance tuning and efficient usage on HPC and novel architectures; introductory tutorials for novel users and much more.
The webinars include an audience Q&A session during which attendees can ask questions and make suggestions. They are a great opportunity to interact with the main code developers.
Webinar: “Atomistic Molecular Dynamics Setup with MDWeb”
Presenter: Adam Hospital
Date: Wednesday, May 25, 2016
Time: 16:00-17:00 CET (Central European Time)
This webinar took place on May 25, 2016. Registration is now closed.
Atomistic Molecular Dynamics Setup with MDWeb
Adam Hospital
Molecular Modeling and Bioinformatics, Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain. National Institute of Bioinformatics (INB), Elixir-ES, Spain.
adam.hospital@irbbarcelona.org
Biological function is largely based on molecular recognition. Biological macromolecules interact to each other following strict rules on the complementarity of 3D structures and interactions. The understanding of molecular recognition has been based traditionally on the analysis of static models of protein and nucleic acids 3D structures as found in the Protein Data Bank (PDB [1]). However, molecular recognition requires precise adjustments of the structures to optimize the binding, what is possible due to the intrinsic flexibility of biological macromolecules, but very difficult to follow using static pictures of those structures. Although some information about flexibility and induced fit could be extracted from the set of conformations available in PDB, only theoretical methods can draw a full picture of the phenomenon [2]. A series of tools and databases offering an integrated approach to study macromolecular flexibility have been developed in IRB Barcelona.
Molecular Dynamics simulations (MD [3,4]) is the most well-known theoretical technique to extract macromolecular flexibility. Unfortunately, its usage has been hindered by its steep learning curve, especially in the first steps of the process: the structure preparation or setup. MDWeb [5] is a web server designed to ease this first contact with MD simulation. Its web-based interface provides a user-friendly workbench where user can graphically check for the quality of the input structure, tailor their own setup protocols, or use a collection of predefined ones. The final generated system, already prepared to run the MD simulation, can be then downloaded.
For those interested in nucleic acids simulations, we developed a specific web interface, NAFlex [6] (powered by MDWeb) adding nucleic acid-specific analysis to the set of functionalities already existing in MDWeb. And using MD simulations and these automatic setup procedures, we were able to populate a couple of trajectory databases (MoDEL [7] for proteins and BIGNASim [8] for nucleic acids).
In this first webinar, we will focus on MDWeb, on how to use the web interface to go from a PDB structure to a completely prepared system (surrounded by solvent and counterions, energetically minimized and equilibrated), ready to be used as input for a MD simulation.
References
1. Berman HM, Battistuz T, Bhat TN, et al. The protein data bank. Acta Crystallogr D Biol Cryst. 2002;58:899–907.
2. Hospital A, Goñi JR, Orozco M, and Gelpí JL. Molecular dynamics simulations: advances and applications. Adv Appl Bioinform Chem, 2015,10:37-47.
3. McCammon JA, Gelin BR, Karplus M. Dynamics of folded proteins. Nature. 1977;267(5612):585–590.
4. Warshel A, Levitt M. Theoretical studies of enzymic reactions – dielectric, electrostatic and steric stabilization of carbonium-ion in reaction of lysozyme. J Mol Biol. 1976;103(2):227–249.
5. Hospital A, Andrio P, Fenollosa C, Cicin-Sain D, Orozco M, Gelpi JL. MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations. Bioinformatics. 2012;28(9):1278–1279.
6. Hospital A, Faustino I, Collepardo-Guevara R, González C, Gelpí JL, and Orozco M. NAFlex: a web server for the study of nucleic acid flexibility. Nucleic Acids Res, 2013 41:W47-55.
7. Meyer T, D’Abramo M, Hospital A, et al. MoDEL (molecular dynamics extended library): a database of atomistic molecular dynamics trajectories. Structure. 2010;18(11):1399–1409.
8. Hospital A, Andrio P, Cugnasco C, Codó L, Becerra Y, Dans PD., Battistini F, Torres J, Goñi JR, Orozco M, Gelp JL. BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data., Nucleic Acids Res, 2016 44( D1):D272-8.
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