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Protocols

MDWeb specifications

Information


Unique identifier OMICS_06521
Name MDWeb
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for MDWeb

MDWeb citations

 (8)
library_books

How accurate are accurate force fields for B DNA?

2017
Nucleic Acids Res
PMCID: 5397185
PMID: 28088759
DOI: 10.1093/nar/gkw1355

[…] During production runs, data was typically collected every 1 ps, which allowed us to study infrequent, but fast movements. Geometrical analysis were carried out with AMBERTOOLS 14 (), GROMACS tools, MDWeb (,,), NaFlex () and the Curves+ package (). As in our recent work (), the 3D-RISM model (, for details see ) was used to compute the SAXS-WAXS spectra (Small-Angle and Wide-Angle X-ray Scatterin […]

library_books

The NS4A Cofactor Dependent Enhancement of HCV NS3 Protease Activity Correlates with a 4D Geometrical Measure of the Catalytic Triad Region

2016
PLoS One
PMCID: 5148068
PMID: 27936126
DOI: 10.1371/journal.pone.0168002

[…] ], using the programs LOOPP [], SWISS-MODEL [–], the CCP4 program suite 6 [, ] the GROMOS96 program, an implementation of the Swiss-pdb viewer [], Procheck, What_Check, ERRAT, Verify_3D, Prove [, –], MDWeb []. […]

library_books

Multiple active site residues are important for photochemical efficiency in the light activated enzyme protochlorophyllide oxidoreductase (POR)☆

2016
PMCID: 4970445
PMID: 27285815
DOI: 10.1016/j.jphotobiol.2016.05.029

[…] ulations by using the Amber ff94 force field implemented in Gromacs 4.6.5. Prior to this, the base structure was corrected and topology files for Gromacs were generated by using the online tools from MDweb . The quality of developed homology model was analyzed using QMEAN server . After optimisation the final model showed a QMEAN score of 0.50 and Z score of 2.95. In addition, the SWISS-MODEL homo […]

call_split

Toll Like Receptor 2 Mediates In Vivo Pro and Anti inflammatory Effects of Mycobacterium Tuberculosis and Modulates Autoimmune Encephalomyelitis

2016
Front Immunol
PMCID: 4878199
PMID: 27252700
DOI: 10.3389/fimmu.2016.00191
call_split See protocol

[…] initial structure for Tlr2 of B6 (where Met was substituted in place of Ile). Model preprocessing for missing H-bond addition and steric classes was done using the built-in algorithms of PDB2PQR and MDWeb. The ligand and other HETAMs were removed during this process. A complete setup for AMBER Parm99SB* forcefield (structure minimization, solvation with TIP3P water molecules, and 50-mM ions and e […]

library_books

Molecular dynamics simulations: advances and applications

2015
PMCID: 4655909
PMID: 26604800
DOI: 10.2147/AABC.S70333

[…] ng language, automation of procedures is not a straightforward task. Lessons learned in the preparation of the MoDEL database, by our group, leaded to the generation of a new set of tools, MDMoby and MDWeb that try to cover both aspects of the problem. On one hand, MDMoby provides a full set of web services, covering all setup, simulation, and analysis operations. The modular nature of such collec […]

library_books

Comparative genomics of closely related Salmonella enterica serovar Typhi strains reveals genome dynamics and the acquisition of novel pathogenic elements

2014
BMC Genomics
PMCID: 4289253
PMID: 25412680
DOI: 10.1186/1471-2164-15-1007

[…] Y (histidine to tyrosine) using FixPDB with the NOMAD-Ref server [] and validated with the SPDB viewer []. The native and mutant structures were checked, fixed, refined and energetically optimised by MDWeb [], ModRefiner [], FG-MD [] and the SPDB viewer []. The qualities of the model structures were independently verified with the PROCHECK [], WHATCHECK [] and PROSA programs []. […]

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

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