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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 in pipeline

2017
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 […]


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MDWeb in publications

 (8)
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 […]

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 []., the molecular dynamics simulations (md) were performed using namd 2.9 under the charmm27 force field for proteins [–] using the same minimization, heating and production methodology […]

PMCID: 5006622
PMID: 27630985
DOI: 10.3389/fbioe.2016.00069

[…] and ligand interacting complex (wallace et al., )., dynamics and stability of the complex between tpor and shortlisted mimetic were evaluated through the molecular dynamics simulations using mdweb program. mdweb is a workspace, which provides standard protocols for molecular dynamics simulations and to scrutinize the interactions trajectories (hospital et al., ). the optimized structure […]

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

[…] 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 […]

PMCID: 4878199
PMID: 27252700
DOI: 10.3389/fimmu.2016.00191

[…] 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 […]


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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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