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Publication for MDWeb
How accurate are accurate force fields for B DNA?
[…] 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 […]
The NS4A Cofactor Dependent Enhancement of HCV NS3 Protease Activity Correlates with a 4D Geometrical Measure of the Catalytic Triad Region
[…] ], 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 . […]
Multiple active site residues are important for photochemical efficiency in the light activated enzyme protochlorophyllide oxidoreductase (POR)☆
[…] 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 […]
Toll Like Receptor 2 Mediates In Vivo Pro and Anti inflammatory Effects of Mycobacterium Tuberculosis and Modulates Autoimmune Encephalomyelitis
[…] 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 […]
Molecular dynamics simulations: advances and applications
[…] 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 […]
Comparative genomics of closely related Salmonella enterica serovar Typhi strains reveals genome dynamics and the acquisition of novel pathogenic elements
[…] 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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