The Biological Structure Model Archive (BSM-Arc): an archive for in silico models and simulations

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Abstract

We present the Biological Structure Model Archive (BSM-Arc, https://bsma.pdbj.org), which aims to collect raw data obtained via in silico methods related to structural biology, such as computationally modeled 3D structures and molecular dynamics trajectories. Since BSM-Arc does not enforce a specific data format for the raw data, depositors are free to upload their data without any prior conversion. Besides uploading raw data, BSM-Arc enables depositors to annotate their data with additional explanations and figures. Furthermore, via our WebGL-based molecular viewer Molmil, it is possible to recreate 3D scenes as shown in the corresponding scientific article in an interactive manner. To submit a new entry, depositors require an ORCID ID to login, and to finally publish the data, an accompanying peer-reviewed paper describing the work must be associated with the entry. Submitting their data enables researchers to not only have an external backup but also provide an opportunity to promote their work via an interactive platform and to provide third-party researchers access to their raw data.

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Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures

Akira Kinjo, Gert-Jan Bekker, Hirofumi Suzuki … (2016)

The Protein Data Bank Japan (PDBj, http://pdbj.org), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins. We herein outline the updated web user interfaces together with RESTful web services and the backend relational database that support the former. To enhance the interoperability of the PDB data, we have previously developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, which is now a wwPDB standard called wwPDB/RDF. We have enhanced the connectivity of the wwPDB/RDF data by incorporating various external data resources. Services for searching, comparing and analyzing the ever-increasing large structures determined by hybrid methods are also described.

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MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories.

Modesto Orozco, Jordi Camps, Ricardo Gelpi … (2010)

More than 1700 trajectories of proteins representative of monomeric soluble structures in the protein data bank (PDB) have been obtained by means of state-of-the-art atomistic molecular dynamics simulations in near-physiological conditions. The trajectories and analyses are stored in a large data warehouse, which can be queried for dynamic information on proteins, including interactions. Here, we describe the project and the structure and contents of our database, and provide examples of how it can be used to describe the global flexibility properties of proteins. Basic analyses and trajectories stripped of solvent molecules at a reduced resolution level are available from our web server. Copyright © 2010 Elsevier Ltd. All rights reserved.

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Dynameomics: a comprehensive database of protein dynamics.

Marc W van der Kamp, R. Schaeffer, Amanda Jonsson … (2010)

The dynamic behavior of proteins is important for an understanding of their function and folding. We have performed molecular dynamics simulations of the native state and unfolding pathways of over 2000 protein/peptide systems (approximately 11,000 independent simulations) representing the majority of folds in globular proteins. These data are stored and organized using an innovative database approach, which can be mined to obtain both general and specific information about the dynamics and folding/unfolding of proteins, relevant subsets thereof, and individual proteins. Here we describe the project in general terms and the type of information contained in the database. Then we provide examples of mining the database for information relevant to protein folding, structure building, the effect of single-nucleotide polymorphisms, and drug design. The native state simulation data and corresponding analyses for the 100 most populated metafolds, together with related resources, are publicly accessible through http://www.dynameomics.org. Copyright 2010 Elsevier Ltd. All rights reserved.

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Author and article information

Contributors

Gert-Jan Bekker:

ORCID: https://orcid.org/0000-0001-8385-5693

gertjan.bekker@protein.osaka-u.ac.jp

Journal

Journal ID (nlm-ta): Biophys Rev

Journal ID (iso-abbrev): Biophys Rev

Title: Biophysical Reviews

Publisher: Springer Berlin Heidelberg (Berlin/Heidelberg )

ISSN (Print): 1867-2450

ISSN (Electronic): 1867-2469

Publication date (Electronic): 5 February 2020

Publication date PMC-release: 5 February 2020

Publication date Collection: April 2020

Volume: 12

Issue: 2

Pages: 371-375

Affiliations

GRID grid.136593.b, ISNI 0000 0004 0373 3971, Institute for Protein Research, , Osaka University, ; 3-2 Yamadaoka, Suita, Osaka 565-0871 Japan

Author information

Gert-Jan Bekker https://orcid.org/0000-0001-8385-5693

Takeshi Kawabata https://orcid.org/0000-0002-0032-9688

Genji Kurisu https://orcid.org/0000-0002-5354-0807

Article

Publisher ID: 632

DOI: 10.1007/s12551-020-00632-5

PMC ID: 7242595

PubMed ID: 32026396

SO-VID: ff8fe5bb-acd9-44fe-9c6f-7494ded69674

License:

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

History

Date received : 15 January 2020

Date accepted : 28 January 2020

Funding

Funded by: Japan Agency for Medical Research and Development (JP)

Award ID: JP19am0101066

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issue-copyright-statement © International Union for Pure and Applied Biophysics (IUPAB) and Springer-Verlag GmbH Germany, part of Springer Nature 2020

ScienceOpen disciplines: Biophysics

Keywords: molecular dynamics,homology modeling,database,archive,raw data,sharing

Data availability:

ScienceOpen disciplines: Biophysics

Keywords: molecular dynamics, homology modeling, database, archive, raw data, sharing

The Biological Structure Model Archive (BSM-Arc): an archive for in silico models and simulations

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Abstract

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Higher order chromatin architecture

Most cited references 16

Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures

MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories.

Dynameomics: a comprehensive database of protein dynamics.

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