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FlexServ: an integrated tool for the analysis of protein flexibility

J. Camps, O. Carrillo, A. Emperador, L. Orellana, A. Hospital, M. Rueda, D. Cicin-Sain, M. D'Abramo, J. L. Gelpi, M. Orozco
2009 Bioinformatics  
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

Adam Hospital
2016 Zenodo  
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

Tim Meyer, Marco D'Abramo, Adam Hospital, Manuel Rueda, Carles Ferrer-Costa, Alberto Pérez, Oliver Carrillo, Jordi Camps, Carles Fenollosa, Dmitry Repchevsky, Josep Lluis Gelpí, Modesto Orozco
2010 Structure  
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

Adam Hospital, Pau Andrio, Carles Fenollosa, Damjan Cicin-Sain, Modesto Orozco, Josep Lluís Gelpí
2012 Computer applications in the biosciences : CABIOS  
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

Adam Hospital, Pau Andrio, Cesare Cugnasco, Laia Codo, Yolanda Becerra, Pablo D. Dans, Federica Battistini, Jordi Torres, Ramón Goñi, Modesto Orozco, Josep Ll. Gelpí
2015 Nucleic Acids Research  
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

Adam Hospital, Ignacio Faustino, Rosana Collepardo-Guevara, Carlos González, Josep Lluis Gelpí, Modesto Orozco
2013 Nucleic Acids Research  
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

Rajni Verma, Ulrich Schwaneberg, Danilo Roccatano
2012 Computational and Structural Biotechnology Journal  
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

Adam Hospital, Anna Montras, Stian Soiland-Reyes, Alexandre Bonvin, Adrien Melquiond, Josep Lluís Gelpí, Daniele Lezzi, Steven Newhouse, Jose A. Dianes, Mark Abraham, Rossen Apostolov, Emiliano Ippoliti (+2 others)
2016 Zenodo  
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

Sheik Amamuddy, Veldman, Manyumwa, Khairallah, Agajanian, Oluyemi, Verkhivker, Tastan Bishop
2020 International Journal of Molecular Sciences  
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

Elena Papaleo, Nicola Casiraghi, Alberto Arrigoni, Marco Vanoni, Paola Coccetti, Luca De Gioia, Franca Fraternali
2012 PLoS ONE  
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

Adam Carter, Ian Harrow, Rossen Apostolov, Stian Soiland-Reyes, Bert de Groot, Mark Abraham
2016 Zenodo  
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

Thomas L Rodgers, David Burnell, Phil D Townsend, Ehmke Pohl, Martin J Cann, Mark R Wilson, Tom CB McLeish
2013 BMC Bioinformatics  
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

Nalini Schaduangrat, Samuel Lampa, Saw Simeon, Matthew Paul Gleeson, Ola Spjuth, Chanin Nantasenamat
2020 Journal of Cheminformatics  
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

Kristin Blacklock, Gennady M. Verkhivker, Rafael Josef Najmanovich
2014 PLoS ONE  
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

Elena Papaleo, Giulia Renzetti, Matteo Tiberti, Franca Fraternali
2012 PLoS ONE  
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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