Suite 2022 1

Manufactured by Schrödinger

Suite 2022-1 is a comprehensive software package designed for computational chemistry and molecular modeling. It includes a variety of tools and algorithms for tasks such as structure generation, conformational analysis, and property prediction. The core function of this suite is to provide researchers with a powerful and flexible platform for exploring the properties and behaviors of molecules and materials.

Automatically generated - may contain errors

Lab products found in correlation

Prime mm gbsa module, by Schrödinger (1 mentions) Prime module, by Schrödinger (1 mentions) Force field builder, by Schrödinger (1 mentions)

Spelling variants of this product

Suite 2022 (3 citations)

3 protocols using suite 2022 1

MM-GBSA Binding Free Energy Calculation

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

Molecular mechanics with generalized Born and surface area solvation (MM‐GBSA) is a largely used physics‐based method to estimate the binding free energy of a ligand bound to a protein.^[49] The Prime module^[27] in the Schrödinger suite 2022‐1^[26] was used to compute MM‐GBSA free energy of binding (ΔG bind) for all compounds bound to MTHFD2 or MTHFD1, using the following equation [Eq. (2)]: 2

Δ G b i n d = E_{C o m p l e x} - E_{L i g a n d} - E_{R e c e p t o r}

where E_Complex, E_Ligand, and E_Receptor represent the energy calculations carried out in the Prime MM GBSA module for the optimized complex (complex), optimized free ligand (ligand), and optimized free receptor (receptor), respectively. The OPLS4 force field^[30] and VSGB solvation model^[50] were employed in the binding free energy calculations. The obtained binding free energies (ΔG Bind), the Coulomb energy contribution (ΔG Coulomb), the Lipophilic energy (ΔG Lipophilic) and the van der Waals energy (ΔG van der Waals) of all compounds are discussed in this work.

Jha V, & Eriksson L.A. (2023). Binding Modes of Xanthine‐Derived Selective Allosteric Site Inhibitors of MTHFD2. ChemistryOpen, 12(5), e202300052.

+ Open protocol

+ Expand

Computational Binding Free Energy Predictions

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

The congeneric series of the ligands studied here were docked onto the IPC and CPI representative frames used in the AB-FEP above, using Glide (46 (link)) with the shape-based constraints (as implemented in Schrodinger suite 2022-1) using the bound Lu AF88273 as a reference. Force Field Builder (31 (link)) (Schrodinger release 2022-1) was used to parametrize any missing torsions found in the congeneric series studied here. The default protocol of RB-FEP as implemented in FEP+ module (30 (link)) was used, wherein 24 lambda windows, as well as 8 Å SPC water buffer, were used for the charged ligands studied here. After a relaxation stage [as described previously (30 (link))], 30-ns production RB-FEP simulations were performed. To assess the consistency of the FEP+ predictions, cycle closure correction (34 (link)) was applied, and the ΔΔG^pred were converted to ΔG^pred using an offset obtained from the experimental ΔG data, as outlined previously (30 (link)). Finally, the perturbations labeled as “bad” by the FEP+ module [specifically those with high hysteresis and large Bennett errors (34 (link))] were removed from the analysis.

Salomon K., Abramyan A.M., Plenge P., Wang L., Bundgaard C., Bang-Andersen B., Loland C.J, & Shi L. (2023). Dynamic extracellular vestibule of human SERT: Unveiling druggable potential with high-affinity allosteric inhibitors. Proceedings of the National Academy of Sciences of the United States of America, 120(41), e2304089120.

+ Open protocol

+ Expand

Binding Energy Analysis of Designed Compounds

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

To study the binding energy of the designed compounds
on targets,
AChE (PDB ID: 4EY7) and BACE-1 (PDB ID: 2ZJM). The Schrodinger Suite 2022–1 protein preparation
wizard tool was utilized to prepare the protein. It consists of three
essential steps: first, the OPLS-2005 force field was used to ascribe
the partial charge after hydrogens were added. The same field was
also used to ascribe the protonated states, and partial energy minimization
was used to regulate the heavy atoms. By destruction of the ligand,
the location for ligand binding was established. The next phase involved
creating ligands using the LigPrep module with the OPLS-2005 force
field and default settings.

Singh A., Verma A., Bhardwaj B., Saraf P., Kumar H., Jain N., Waiker D.K., Gajendra T.A., Krishnamurthy S, & Shrivastava S.K. (2024). Structure-Guided Design, Synthesis, and Biological Evaluation of Peripheral Anionic Site Selective and Brain Permeable Novel Oxadiazole-Piperazine Conjugates against Alzheimer’s Disease with Antioxidant Potential. ACS Omega, 9(16), 18169-18182.

+ 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!