Schrödinger’s Maestro program (version 9.3.5) was used as the primary graphical user interface and Release 2015-2: Maestro, version 10.2 (Schrödinger, LLC, New York, NY) was used for ligand interaction diagramming [8 ]. Docking of diC4-PIP3 on a grid centered at the C5 term NT (site1) of hsortilin crystal structure at excess concentration of NT PDB ID: 4PO7 was performed using Schrödinger’s Glide software [9 (link)] as described [5 (link)].
Maestro program
Manufactured by Schrödinger
Sourced in United States
Maestro is a computational chemistry software program developed by Schrödinger. It serves as a platform for molecular modeling, simulations, and data analysis. The core function of Maestro is to provide a comprehensive suite of tools for researchers to build, visualize, and analyze molecular structures and their properties.
Automatically generated - may contain errors
Lab products found in correlation
Ligprep program, by Schrödinger (3 mentions)
Glide software, by Schrödinger (2 mentions)
Maestro version 10, by Schrödinger (2 mentions)
Prime program, by Schrödinger (1 mentions)
Vina v1, by AutoDock (1 mentions)
Protein preparation wizard panel, by Schrödinger (1 mentions)
Opls 2005 force field, by Schrödinger (1 mentions)
Macromodel, by Schrödinger (1 mentions)
Prime software, by Schrödinger (1 mentions)
17 protocols using maestro program
1
Docking of diC4-PIP3 on hsortilin
2
Molecular Docking Analysis of HCs-Cx46-CBX/ENX
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The HCs-Cx46-CBX/ENX interaction analysis was performed in the AutoDock Vina v1.2.3 program [73 (link)]. The interaction parameters were made keeping the protein rigid and the ligands as flexible molecules. In addition to this, a screening box or “Grid Box” with specific dimensions centered on the “interaction pocket” was generated using the AutoDock tools program. The generated complexes were classified according to the affinity constants predicted in kcal/mol. The analysis of the HCs-Cx46-CBX/ENX interface and the energetic parameters were performed in the Maestro program (Schrödinger, LLC, New York, NY, USA, 2016). Additionally, the theoretical Δgbind was calculated through the MM-GBSA energy calculation using the Prime program (Schrödinger, LLC, New York, NY, USA, 2016). All images were created in PyMOL v1.7 [107 ].
3
Molecular Docking of Phytocompounds with SARS-CoV-2 RdRp
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
To study the mode of interactions of phytocompounds in the defined binding site of SARS-CoV-2 RdRp, molecular docking was performed using FlexX software (LeadIT 2.3.2).65 (link),66 (link) This software uses an incremental buildup algorithm guiding the flexible placement of ligand in the binding region.67 (link)
FlexX considers ligand flexibility by changing the conformations of the ligand in the active site while making the protein rigid.68 (link)
It is an extremely fast, robust, and highly configurable computer program for predicting protein-ligand interactions.69 (link)
The SDF file of the compounds was uploaded in FlexX as a docking library. FlexX default docking parameters were kept with 200 conformations per iteration and maintained conformation per fragmentation. The top-ranked poses were selected for the interaction study, the FlexX rank the resulting docked poses as per the FlexX score (docking energy). The intermolecular interactions between the SARS-CoV-2 RdRp and ligands were studied using the Maestro program (Schrodinger Release 2020-3: Maestro). Binding poses of the ligands visualized in Maestro were selected for further studies based on their binding affinity and mode of interactions with SARS-CoV-2 RdRp. Subsequently, the compounds were subjected to 100 ns MD simulation to probe the binding stability.
FlexX considers ligand flexibility by changing the conformations of the ligand in the active site while making the protein rigid.68 (link)
It is an extremely fast, robust, and highly configurable computer program for predicting protein-ligand interactions.69 (link)
The SDF file of the compounds was uploaded in FlexX as a docking library. FlexX default docking parameters were kept with 200 conformations per iteration and maintained conformation per fragmentation. The top-ranked poses were selected for the interaction study, the FlexX rank the resulting docked poses as per the FlexX score (docking energy). The intermolecular interactions between the SARS-CoV-2 RdRp and ligands were studied using the Maestro program (Schrodinger Release 2020-3: Maestro). Binding poses of the ligands visualized in Maestro were selected for further studies based on their binding affinity and mode of interactions with SARS-CoV-2 RdRp. Subsequently, the compounds were subjected to 100 ns MD simulation to probe the binding stability.
4
Molecular Dynamics Simulation of MK5
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The simulations were analysed using the Maestro program of the Schrödinger suite of programs. The Root Mean Square Deviations (RMSD) from the initial structure and the root mean square fluctuations (RMSF) were calculated during all MD simulations. All atoms were included in the calculations of the RMSF. Atomic distances important for ligand binding and structural changes in MK5 were calculated for all the simulations.
5
Molecular Dynamics Analysis of ADA1 Structure
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The three-dimensional (3D) structure of human ADA1 (PDB code: 3IAR) was used in the in silico analysis. Molecular dynamics (MD) simulations of ADA1 and docking studies were carried out according to a method described previously (Handa et al. 2013 (link)). Briefly, MD simulations of the 3D structure were carried out with a Maestro program from the Schrödinger Suite 2010 (Schrödinger K.K., Tokyo, Japan). Minimizations of the protein structure were carried out using force field OPLS_2005 until the average root-mean-square deviation (RMSD) of the heavy atoms reached 0.3 Å. The two-dimensional (2D) structure of naringin was converted into the 3D structure using the LigPrep program from the Schrödinger Suite 2010. The final step of a LigPrep preparation was an energy minimization of the 3D conformers using OPLS_2005. For conformational search of the compound, the CongGen program from the Schrödinger Suite 2010 was used. The computational docking was carried out using the Glide SP docking program from the Schrödinger Suite 2008 (Schrödinger K.K.).
6
In-silico Analysis of Antibody Structures
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
For the purpose of in-silico analysis, the 3D structures of both proteins (MW ∼ 150 kDa) were generated by homology modeling. Antibody sequences were used as an input for homology modelling in Maestro program within Schrödinger suite (Release 2021–2, Schrödinger, LLC, New York, NY). Templates for Fv region were selected based on sequence identity. The framework for complete antibody modelling was selected based on IgG type. Hydrophobic interaction chromatography (HIC) retention factors were obtained from the literature [13] (link). Surface aggregation propensity score was calculated using an in-house implementation of the algorithm using Python and PyMOL [14] (link). The isoelectric points were obtained from the literature [15] (link). The net charge was calculated for the protein homology models using PROPKA3. Spatial charge map was calculated for the protein homology models using an in-house implementation of the algorithm using Python and PyMOL [16] (link).
7
Structural Modeling of Sfh5 with PtdIns
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Protein models were prepared using the Protein Preparation Wizard panel in the Schrödinger suite (2018–1, Schrodinger, LLC, Mew York, NY, 2018). The Sfh5 structure was optimized with the OPLS_2005 forcefield in the Schrödinger suite to relieve all atom and bond strains found after adding all missing side chains and/or atoms. The Sfh5::PtdIns model was generated by structural overlay of Sfh1::PtdIns complex (PDB ID 3B7N; Schaaf et al., 2008 (link)) on Sfh5 monomer. The heme group of Sfh5 was replaced by PtdIns, which was extracted from Sfh1. The Sfh5::PtdIns complex was energy minimized to relieve Sfh5 and PtdIns atoms of any van der Waal steric clashes and complex was optimized for electrostatic interactions. Molecular graphics and analyses were performed with UCSF Chimera and Schrödinger’s Maestro program.
8
Molecular Dynamics Simulation of Protein Structures
9
Docking Studies Using Glide Program
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Docking studies were performed with the Glide [33 (link),34 (link),35 ] program from the Schrodinger suits using the XP protocol. Docking grid generation was based on X-ray crystal structure as it was deposited into the Protein Database (pdb code: 3S79) and refined by the Protein Preparation Wizard. During the XP docking calculations, enhanced sampling was selected and the energy window for ring sampling was also increased to 100 kcal/mol and the number of final outputs per ligand was enlarged to 10. All figures were prepared with the Maestro program [35 ] which is the GUI part of the Schrödinger program package.
10
Modeling HIV Integrase Binding Site
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The LEDGF binding site construct of HIV integrase was prepared as previously reported (Gallicchio et al., 2014 (link)). Water molecules, bound ligands, and crystallization ions were removed and protein sidechain protonation states were assigned assuming pH 7 and absence of significant pKa shifts (Glu and Asp deprotonated and Lys and Arg protonated). A key residue in the LEDGF binding site, His171, was protonated at the Nδ position as previously investigated (Gallicchio et al., 2014 (link)). The cyclic SLKIDNLD peptide was adapted from the crystal structure of HIV integrase from which it was bound, 3AVB, as formerly reported (Rhodes et al., 2011 (link)). Four cyclic mutants (ALKIDNLD, ALKIDNMD, SLKINNLD, and SLKADNLD) in addition with a linear peptide H-SLKIDNLD-OH were constructed by modifying the cyclic SLKIDNLD peptide using the Maestro program (Schrödinger, LLC).
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!