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FlexServ: an integrated tool for the analysis of protein flexibility
2009
Bioinformatics
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FlexServ is a web-based tool for the analysis of protein flexibility. ...
The server incorporates powerful protocols for the coarsegrained determination of protein dynamics using different versions of Normal Mode Analysis (NMA), Brownian dynamics (BD) and Discrete Dynamics ( ...
Conflict of Interest: none declared. ...
doi:10.1093/bioinformatics/btp304
pmid:19429600
fatcat:g7zc6ixjxveapfzkx2hqjckmy4
BioExcel Webinar #3 - Atomistic Molecular Dynamics Setup with MDWeb
2016
Zenodo
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A series of tools and databases offering an integrated approach to study macromolecular flexibility have been developed in IRB Barcelona. ...
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]). ...
• MD & Flexibility: FlexServ, NAFlex. ...
doi:10.5281/zenodo.3775862
fatcat:efengya4wbghngwhwnm4xshbou
MoDEL (Molecular Dynamics Extended Library): A Database of Atomistic Molecular Dynamics Trajectories
2010
Structure
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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. ...
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 ...
Sergi Girona and the MareNostrum support team for making this project possible. Helpful comments from Prof. F. J. Luque and many colleagues at IRB Barcelona and the BSC are gratefully acknowledged. ...
doi:10.1016/j.str.2010.07.013
pmid:21070939
fatcat:jyc64i63grap5hvenuwwjppvyu
MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations
2012
Computer applications in the biosciences : CABIOS
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Tools for analysis of trajectories, either provided by the user or retrieved from our MoDEL database (http://mmb.pcb.ub.es/MoDEL) are also incorporated. ...
It provides inputs and can send simulations for three of the most popular MD packages (Amber, NAMD and Gromacs). ...
ACKNOWLEDGEMENT We are indebted all the beta-testers of the platform. ...
doi:10.1093/bioinformatics/bts139
pmid:22437851
fatcat:hbp74nj5jfh63ebhqq3yy7ieea
BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data
2015
Nucleic Acids Research
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The database is based on the combination of two NoSQL engines, Cassandra for storing trajectories and MongoDB to store analysis results and simulation metadata. ...
Several projects to generate stable trajectory databases have been developed for proteins, but no equivalence exists in the nucleic acids world. ...
ACKNOWLEDGEMENTS We are indebted to the members of the ABC consortium for many discussions, and the parmBSC1 contributors for the BIGNASim initial data set. ...
doi:10.1093/nar/gkv1301
pmid:26612862
pmcid:PMC4702913
fatcat:ro7nte3jfraordioubebyzt3fa
NAFlex: a web server for the study of nucleic acid flexibility
2013
Nucleic Acids Research
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We present NAFlex, a new web tool to study the flexibility of nucleic acids, either isolated or bound to other molecules. ...
The trajectories obtained by simulations, or imported externally, can be visualized and analyzed using a large number of tools, including standard Cartesian analysis, essential dynamics, helical analysis ...
Dans for their extensive testing of the platform, P. Sfriso for his help in NOE intensity computation, P. Andrio for his help in the design of the graphical interface and J. ...
doi:10.1093/nar/gkt378
pmid:23685436
pmcid:PMC3692121
fatcat:rgzxoxlrffafpnieq2jxwozncm
COMPUTER-AIDED PROTEIN DIRECTED EVOLUTION: A REVIEW OF WEB SERVERS, DATABASES AND OTHER COMPUTATIONAL TOOLS FOR PROTEIN ENGINEERING
2012
Computational and Structural Biotechnology Journal
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Both cases depend on the nature of the problem and show high success rate only for the prediction of single or double site mutations. ...
The first approach employs the information of protein structure and focuses mutagenesis to modify protein scaffolds (e.g. the active site of the biocatalyst). ...
Acknowledgements We thank European Community's Seventh Framework Program EU-FP7 (OXYGREEN project, grant agreement no. 212281) for the financial support.
Citation ...
doi:10.5936/csbj.201209008
pmid:24688649
pmcid:PMC3962222
fatcat:5vh7hlzklrf35plaiaz7fgry2m
Bioexcel Deliverable 2.1 – State Of The Art And Gap Analysis
2016
Zenodo
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This deliverable describes the state of the art and gives a technological gap analysis in the portable environments for computing and data resources of BioExcel. ...
For the interoperability issue, we found that the need for manual interaction needs to be reduced, for instance by incorporating workflow managers to integrate processes and input/output data. ...
NAFlex NAFlex is a web tool for the analysis of nucleic acids flexibility, both isolated and protein-bound. ...
doi:10.5281/zenodo.263963
fatcat:o2v7ogjmnbauhn7txp2buz3pem
Integrated Computational Approaches and Tools for Allosteric Drug Discovery
2020
International Journal of Molecular Sciences
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As such, the critical analysis and integration ofestablished approaches into robust, reproducible, and customizable computational pipelines withexperimental feedback could make allosteric drug discovery ...
In this article,we review computational approaches for allosteric drug discovery and discuss how these tools can beutilized to develop consensus workflows for in silico identification of allosteric sites ...
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. ...
doi:10.3390/ijms21030847
pmid:32013012
pmcid:PMC7036869
fatcat:y2z5vnsylnduhc7gntjkpcoslq
Loop 7 of E2 Enzymes: An Ancestral Conserved Functional Motif Involved in the E2-Mediated Steps of the Ubiquitination Cascade
2012
PLoS ONE
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In the successive steps, L7 conserved acidic residues also provide an interaction interface for both Ub and the Rbx1 RING subdomain of the cognate E3. ...
The ubiquitin (Ub) system controls almost every aspect of eukaryotic cell biology. Protein ubiquitination depends on the sequential action of three classes of enzymes (E1, E2 and E3). ...
Ruth Nussinov for her extremely valuable comments and the careful reading of the manuscript, as well as Ilaria Valimberti and Valeria Ranzani for their involvement in the preliminary phases of the project ...
doi:10.1371/journal.pone.0040786
pmid:22815819
pmcid:PMC3399832
fatcat:tsxtyks6c5ecbhzufs4gt6xdyy
Bioexcel Deliverable 3.1 - Selection And Establishment Of User Groups
2016
Zenodo
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Webinars will also form an important part of the user engagement process and GoToWebinar has been selected as the platform for this function. ...
Additional tools and activities such as blogs and real- time chat will be provided in response to the needs of the groups. ...
dynamics, FlexServ
(http://mmb.irbbarcelona.org/FlexServ), to run a complete set of flexibility
analyses
on
protein
structure
MD
trajectories,
and
NAFlex
(http://mmb.irbbarcelona.org/NAFlex) ...
doi:10.5281/zenodo.264011
fatcat:iqowqfjwozhmlmlvmm3iin4jxi
ΔΔPT: a comprehensive toolbox for the analysis of protein motion
2013
BMC Bioinformatics
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Normal Mode Analysis is one of the most successful techniques for studying motions in proteins and macromolecules. ...
Results: PT is a toolbox allowing calculation of elastic network models and principle component analysis. It allows the analysis of pdb files or trajectories taken from; Gromacs, Amber, and DL_POLY. ...
Tool Description
Conclusions NMA is a powerful tool for the study of protein movements, conformational changes, and protein entropy. ...
doi:10.1186/1471-2105-14-183
pmid:23758746
pmcid:PMC3689072
fatcat:ua4zrggi65c43e7frtu5ezetiu
Towards reproducible computational drug discovery
2020
Journal of Cheminformatics
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This article provides an in-depth coverage on the reproducibility of computational drug discovery. ...
It is therefore inevitable that the field of computational drug design would adopt an open approach towards the collection, curation and sharing of data/code. ...
Sirarat Sarntivijai from the European Bioinformatics Institute and Dr. Likit Preeyanon from the Department of Community Medical Technology for fruitful discussions. ...
doi:10.1186/s13321-020-0408-x
pmid:33430992
fatcat:bvdcvjhi4jhlnifpc25t6cjthq
Allosteric Regulation of the Hsp90 Dynamics and Stability by Client Recruiter Cochaperones: Protein Structure Network Modeling
2014
PLoS ONE
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Protein network analysis of the essential conformational space of the Hsp90-cochaperone motions has identified structurally stable interaction communities, interfacial hubs and key mediating residues of ...
The network analysis has recapitulated a broad range of structural and mutagenesis experiments, particularly clarifying the elusive role of Rar1 as a regulator of the Hsp90 interactions and a stability ...
Hsp90 is an abundant and highly specialized molecular chaperone that is essential for the integrity of many signaling pathways. ...
doi:10.1371/journal.pone.0086547
pmid:24466147
pmcid:PMC3896489
fatcat:z3u2vzxoqfavleafkrf52k37ui
Mechanisms of Intramolecular Communication in a Hyperthermophilic Acylaminoacyl Peptidase: A Molecular Dynamics Investigation
2012
PLoS ONE
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Protein dynamics and the underlying networks of intramolecular interactions and communicating residues within the threedimensional (3D) structure are known to influence protein function and stability, ...
In the present contribution, protein dynamics signatures of a hyperthermophilic acylaminoacyl peptidase (AAP) of the prolyl oligopeptidase (POP) family, as well as of a deletion variant and alanine mutants ...
Luca De Gioia for careful reading of the manuscript and his suggestions, along with Alberto Arrigoni for all the fruitful comments and the technical assistance in several steps of this work. ...
doi:10.1371/journal.pone.0035686
pmid:22558199
pmcid:PMC3338720
fatcat:pk6gj57fmzc6zfl6udtujzzrgq
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