Maestro version 10

Manufactured by Schrödinger

Sourced in United States

Maestro version 10.2 is a computational chemistry software suite that provides a comprehensive platform for molecular modeling, simulation, and analysis. The software offers a wide range of tools and capabilities for studying the properties and behaviors of chemical systems at the molecular level.

Automatically generated - may contain errors

Lab products found in correlation

Maestro program, by Schrödinger (2 mentions) Ligprep program, by Schrödinger (2 mentions) Epik 2, by Schrödinger (2 mentions) Maestro, by Schrödinger (1 mentions) Prime software, by Schrödinger (1 mentions) Glide software, by Schrödinger (1 mentions) Ligprep module, by Schrödinger (1 mentions) Suite 2015 1, by Schrödinger (1 mentions)

14 protocols using maestro version 10

Elucidating HBV-RT Inhibition Mechanisms

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

To gain insights into the atomic details of the inhibitory mechanism of ETV and CdFA, we built initial molecular models of the ternary complexes of HBV-RT_WT and RT containing three amino acid substitutions, with primer-templates and in complex with ETV-triphosphates (TP) using homology modeling, semi-empirical quantum chemical methods and molecular dynamics as previously described (Takamatsu et al., 2015 (link)). Structural manipulations to generate CdFA-TP as well as to generate different mutated RT residues were performed using Maestro version 10.7.015 (Schrödinger, LLC, New York). Correct bond orders of the residues, including zero-order bonds from the Mg²⁺ to the phosphate groups were assigned, and the termini were capped. Restrained minimization using OPLS3 force field was performed. A cut-off distance of 3.0 Å between a polar hydrogen and an oxygen or nitrogen atom, a minimum donor angle of 60° between D-H-A and a minimum acceptor angle of 90° between H-A-B was used to define the presence of hydrogen bonds (D, A, B are donor, acceptor, and atom connected to acceptor, respectively). Connolly molecular surfaces for the inhibitors and selected RT residues from the active site were generated using a water sphere with a radius of 1.4Å as a probe. Structural figures were generated using Maestro version 10.7.015 (Schrödinger, LLC, New York).

Hayashi S., Higashi-Kuwata N., Das D., Tomaya K., Yamada K., Murakami S., Venzon D.J., Hattori S.I., Isogawa M., Sarafianos S.G., Mitsuya H, & Tanaka Y. (2020). 7-Deaza-7-fluoro modification confers on 4’-cyano-nucleosides potent activity against entecavir/adefovir-resistant HBV variants and favorable safety. Antiviral research, 176, 104744.

+ Open protocol

+ Expand

In silico Analysis of Leishmania Therapeutic Targets

Check if the same lab product or an alternative is used in the 5 most similar protocols

The amino acid
sequences of the target proteins of L. donovani cytoplasmic l-asparaginase-1-like protein (CBZ32861.1), L. donovani metacaspase-2 (ABD19718.1), L. donovani metacaspase-1 (ABD19717.1), and L. donovani DNA topoisomerase II (AAD34021.1) were
retrieved using the database of NCBI (www.ncbi.nlm.nih.gov/).
For interaction analysis of the selected target proteins and ligands,
Schrodinger’s software is used (Schrödinger Release:
Maestro, version 10.5, Schrödinger, LLC, NY 2016-1, USA). This
master software consists of more than one suite that is capable of
performing visualization of the structure, binding site prediction,
and receptor–ligand interaction.

Chandra Pandey S., Dhami D.S., Jha A., Chandra Shah G., Kumar A, & Samant M. (2019). Identification of trans-2-cis-8-Matricaria-ester from the Essential Oil of Erigeron multiradiatus and Evaluation of Its Antileishmanial Potential by in Vitro and in Silico Approaches. ACS Omega, 4(11), 14640-14649.

+ Open protocol

+ Expand

Binding Site Identification for Allosteric Inhibitors

Check if the same lab product or an alternative is used in the 5 most similar protocols

To find out the allosteric site for non-competitive and uncompetitive inhibitors, site recognition software SiteMap 3.7 [49 (link), 50 ] Maestro version 10.5 from Schrödinger was run on crystal structure to identify the top 5 ranked potential ligand-binding pockets.
The grid box with dimensions of 15Ǻ x 15Ǻ x 15Ǻ was defined to confine the mass of centre of each docked ligand. Extra precision (XP) mode of Glide based on OPLS-2005 force field was run for rigid receptor docking protocol [51 –54 (link)]. Molecular mechanics-generalized Born surface area (MM-GBSA) method in Prime was used for rescoring the docked pose of ligand [55 ]. These poses were taken as inputs for the energy minimization of the protein–ligand complexes (E_complex), the free protein (E_receptor), and the free ligands (E_ligand). The binding free energy ΔG_bind was determined according to the following equation:

{Δ G}_{b i n d} = E_{c o m p l e x (m i n i m i z e d)} - E_{l i g a n d (m i n i m i z e d)} - E_{r e c e p t o r (m i n i m i z e d)}

Javaid S., Shaikh M., Fatima N, & Choudhary M.I. (2019). Natural compounds as angiogenic enzyme thymidine phosphorylase inhibitors: In vitro biochemical inhibition, mechanistic, and in silico modeling studies. PLoS ONE, 14(11), e0225056.

+ Open protocol

+ Expand

Molecular Dynamics Simulations Using Schrödinger Suite

Check if the same lab product or an alternative is used in the 5 most similar protocols

All calculations were performed using the Schrödinger Suite through the Maestro graphical interface [Maestro, version 10.5, Schrödinger, LLC, New York, NY, 2016].

Ferrazzano L., Corbisiero D., Potenza E., Baiula M., Dattoli S.D., Spampinato S., Belvisi L., Civera M, & Tolomelli A. (2020). Side chain effect in the modulation of αvβ3/α5β1 integrin activity via clickable isoxazoline-RGD-mimetics: development of molecular delivery systems. Scientific Reports, 10, 7410.

+ Open protocol

+ Expand

Structural Modeling of HIV-1 RT Complexes

Check if the same lab product or an alternative is used in the 5 most similar protocols

Crystal structure of the ternary complexes of HIV-1 RTs with primer-templates (pt) and EFdA-triphosphates (EFdA-TP) reported by Salie etal. (PDB [RRID: SCR_012820] ID: 5J2M) was used as the starting structure (Salie et al., 2016 (link)). Correct bond orders of the residues, including zero-order bonds from the Mg²⁺ to the phosphate groups were assigned, and the termini were capped. A restrained minimization was performed (5J2M_prep). All subsequent minimizations were carried out from the 5J2M_prep structure. MAdA-TP, FMAdA-TP and EtAdA-TP-were built by appropriate modifications to EFdA in 5J2M_prep, and the structures were minimized to obtain respective wild-type complexes. M184 residue was mutated to valine and minimized to obtain respective HIV-1 RT^M184V complexes. Maestro version 10.7.015 (Schrodinger, LLC. New York, NY) was used for molecular model building, visualization, analysis, and figure generation. The OPLS3 forcefield, as implemented in Maestro was used for all structure minimizations.

Takamatsu Y., Das D., Kohgo S., Hayashi H., Delino N.S., Sarafianos S.G., Mitsuya H, & Maeda K. (2018). The high genetic barrier of EFdA/MK-8591 stems from strong interactions with the active site of drug-resistant HIV-1 reverse transcriptase. Cell chemical biology, 25(10), 1268-1278.e3.

+ Open protocol

+ Expand

Molecular Docking for MAO Inhibitor Binding

Check if the same lab product or an alternative is used in the 5 most similar protocols

Molecular docking studies were carried to identify the binding affinities and interaction between the inhibitors and the target proteins (Mono Amine Oxidase) MAO-A and MAO-B using Glide software (Schrodinger Inc. U.S.A.- Maestro version 10.2). Grid-based Ligand Docking with Energetic (Glide) is one of the most accurate docking tool available for ligand–protein, protein–protein binding studies. Glide was found to produce least number of inaccurate poses and 85 % of Glides binding models had an RMSD of 1.4 A^° or less from native co-crystallized structures.

Margret A.A., Begum T.N., Parthasarathy S, & Suvaithenamudhan S. (2015). A Strategy to Employ Clitoria ternatea as a Prospective Brain Drug Confronting Monoamine Oxidase (MAO) Against Neurodegenerative Diseases and Depression. Natural Products and Bioprospecting, 5(6), 293-306.

+ Open protocol

+ Expand

Sortilin Receptor Virtual Screening

Check if the same lab product or an alternative is used in the 5 most similar protocols

Schrödinger’s Maestro program (version 9.3.5) was used as the primary graphical user interface and Maestro version 10.2 (Schrödinger, LLC) was used for ligand interaction diagramming. Virtual screening was performed on compounds contained in ChemBridge libraries (www.chembridge.com) that were prepared with Schrödinger’s LigPrep program (Schrödinger, LLC). The virtual screening method was performed using Schrödinger’s GLIDE software^{29 (link)} on the sortilin crystal structure PDB ID: 4PO7 27. Compounds were docked on grids generated with Glide with cpd541 docked at a box determined by C-terminal NT and cpd984 docked at a box determined by the N-terminal fragment of NT. Grids were then adapted from alignment of PDB ID:6EHO to PDB ID: 4PO7 and docking performed for all grids using Glide XP setting with results exported into GraphPad Prism.

Sparks R.P., Arango A.S., Jenkins J.L., Guida W.C., Tajkhorshid E., Sparks C.E., Sparks J.D, & Fratti R.A. (2020). An Allosteric Binding Site on Sortilin Regulates the Trafficking of VLDL, PCSK9 and LDLR in Hepatocytes. Biochemistry, 59(45), 4321-4335.

+ Open protocol

+ Expand

Virtual Screening for Sortilin Ligands

Check if the same lab product or an alternative is used in the 5 most similar protocols

Schrödinger’s Maestro program (version 9.3.5) was used as the primary graphical user interface and Maestro version 10.2 (Schrödinger, LLC, New York, NY) was used for ligand interaction diagramming. Virtual screening was performed on compounds contained in ChemBridge libraries (www.chembridge.com) that were prepared with Schrödinger’s LigPrep program [14 ]. The virtual screening method was performed using Schrödinger’s GLIDE software [15 (link)] on the hsortilin crystal structure PDB ID: 4PO7 [16 (link)]. Compounds were docked using GLIDE at the site where the N-terminal fragment of NT is found in the crystal structure and cpd984 was chosen for biological screening based on its docking score. Schrödinger’s PRIME software was used to generate missing side chains and loops of this crystal structure predicting the NT peptide spanning the cavity of hsortilin [17 (link)]. LigPrep was used on the N-terminal peptide XLYEN-OH from this crystal structure and it was then docked back into its respective site on the crystal structure. This self-docking task was able to reproduce the X-ray pose for this ligand.

Sparks R.P., Guida W.C., Sowden M.P., Jenkins J.L., Starr M.L., Fratti R.A., Sparks C.E, & Sparks J.D. (2016). Sortilin facilitates VLDL-B100 secretion by insulin sensitive McArdle RH7777 cells. Biochemical and biophysical research communications, 478(2), 546-552.

+ Open protocol

+ Expand

Optimized FDA-approved Drug Structures

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

The FDA-approved drugs from different databases, like the Zinc,^{22 (link)} Superdrug,^{23 (link)} Sweetlead,^{24 (link)} and ChemSpider^{25 (link)} databases, were merged to remove redundancies. The 3D structures generated using the Maestro version 10.2 (Schrödinger)²⁶ were optimized using the LigPrep module (v3.4, Schrödinger 2015-2).²¹ Partial atomic charges were ascribed, and possible ionization states were generated at a pH of 7.0 using the OPLS_2005 force field for optimization and production of low-energy conformers of the ligands.^{27 (link)} Energy minimization was performed for every ligand till it reached a root mean square deviation (RMSD) cutoff of 0.01 Å. Following LigPrep, the compounds were converted into a phase dataset format for input for pharmacophore-based virtual screening.^{28,29 (link)}

Behera D.U., Gaur M., Sahoo M., Subudhi E, & Subudhi B.B. (2023). Development of pharmacophore models for AcrB protein and the identification of potential adjuvant candidates for overcoming efflux-mediated colistin resistance. RSC Medicinal Chemistry, 15(1), 127-138.

+ Open protocol

+ Expand

Computational Molecular Modeling Protocol

Check if the same lab product or an alternative is used in the 5 most similar protocols

All in silico analysis including Glide docking, induced fit docking (IFD), and molecular dynamics (MD) were performed using Schrödinger LLC Maestro version 10.2 [35 ].

Julius A., Renuka R.R., Hopper W., Babu Raghu P., Rajendran S., Srinivasan S., Dharmalingam K., Alanazi A.M., Arokiyaraj S, & Prasath S. (2022). Inhibition of Aldose Reductase by Novel Phytocompounds: A Heuristic Approach to Treating Diabetic Retinopathy. Evidence-based Complementary and Alternative Medicine : eCAM, 2022, 9624118.

+ Open protocol

+ Expand

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?

Revolutionizing how scientists
search and build protocols!