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FlexServ specifications

Information


Unique identifier OMICS_06518
Name FlexServ
Interface Web user interface
Restrictions to use None
Input data A structure in PDB or a sequence in FASTA format
Input format PDB, FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Publication for FlexServ

FlexServ citations

 (6)
library_books

Allosteric Regulation of the Hsp90 Dynamics and Stability by Client Recruiter Cochaperones: Protein Structure Network Modeling

2014
PLoS One
PMCID: 3896489
PMID: 24466147
DOI: 10.1371/journal.pone.0086547

[…] nsecutive pairs of particles,  = 8 Å and  = 0.1 were used.The dMD trajectories were used to compute the force constant values for each residue as was originally introduced in and implemented in the FlexServ web-based tool . A force constant for each residue is calculated by averaging the distances between the residues over the dMD trajectory using the following expression:(3)(4)Here is the inst […]

library_books

Exploring Early Stages of the Chemical Unfolding of Proteins at the Proteome Scale

2013
PLoS Comput Biol
PMCID: 3861036
PMID: 24348236
DOI: 10.1371/journal.pcbi.1003393

[…]  = 1 atm) using the Langevin thermostat and barostats , . The trajectories were analyzed using VMD [44] and the MdWeb server [29], as well as Flexserver which can be accessed at: http://mmb.pcb.ub.es/FlexServ/ (see also Suppl. for a detailed explanation of the metrics). […]

library_books

ΔΔPT: a comprehensive toolbox for the analysis of protein motion

2013
BMC Bioinformatics
PMCID: 3689072
PMID: 23758746
DOI: 10.1186/1471-2105-14-183

[…] s the scaled frequency, fluctuations, and shapes of calculated normal modes; ANM web server [] provides calculation of the normal modes and allows on-line display of the modes with a Jmol plugin; and FlexServ [] provides calculation of normal modes, and also allows simulation by discrete molecular dynamics and Brownian dynamics.There are also programmatic libraries available for analysis of NMA an […]

library_books

Computer Aided Protein Directed Evolution: a Review of Web Servers, Databases and other Computational Tools for Protein Engineering

2012
Comput Struct Biotechnol J
PMCID: 3962222
PMID: 24688649
DOI: 10.5936/csbj.201209008

[…] o [] and [email protected] [] servers are reported here to complete the information about NMA based tools. Both the servers perform NMA using coarse grain model to analyze the conformational changes in protein. FlexServ [] server estimates protein flexibility using three different coarse-grained approaches: 1) discrete molecular dynamics (DMD), 2) normal mode analysis (NMA) and 3) Brownian dynamics (BD). The […]

library_books

Loop 7 of E2 Enzymes: An Ancestral Conserved Functional Motif Involved in the E2 Mediated Steps of the Ubiquitination Cascade

2012
PLoS One
PMCID: 3399832
PMID: 22815819
DOI: 10.1371/journal.pone.0040786

[…] models of E2-f3 enzymes. In particular 3 different coarse-grained algorithms have been used: normal mode analysis (NMA), Brownian dynamics (BD) and discrete dynamics (DMD), as they are implemented in FlexServ , which assumes a coarse-grained representation of the protein (Cα-only). In particular, NMA and BD consider that the inter-residue interactions are controlled by a harmonic-like potential en […]

library_books

Mechanisms of Intramolecular Communication in a Hyperthermophilic Acylaminoacyl Peptidase: A Molecular Dynamics Investigation

2012
PLoS One
PMCID: 3338720
PMID: 22558199
DOI: 10.1371/journal.pone.0035686

[…] elations allow to highlight residues which are characterized by long range communication through the calculation of intermediate correlations. The same algorithm for chained correlations developed in FlexServ was employed. According to this method, starting from a root residue the w highest correlated residues (w = width parameter for the search) are identified for d selected iterations (d = dept […]


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FlexServ institution(s)
Joint IRB-BSC Program on Computational Biology, Institute of Research in Biomedicine, Barcelona Science Park, Barcelona and Barcelona Supercomputing Centre, Spain

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