Structural Optimization and Docking of SOX Derivatives

The two-dimensional structures of synthesized SOX derivatives were drawn with the help of ChemDraw Professional v15.1 and subjected to prepare a three-dimensional structure with the help of Chem3D v15.1. The structural modification, geometrical correction, and optimization were performed with the help of Merck Molecular Force Field (MMFF94). Protoss is an online tool that automatically predicts hydrogens for the interaction between protein-ligand complexes (https://proteins.plus/), accessed on 5 February 2022. The substituted SOXs were subjected to a single-step minimization by the steepest descent method for 500 steps and an RMS gradient of 0.01 [85 (link)]. To perform docking analysis, the eutectic state of protonation of the ligands was found at pH 7.4.

Free full text: Click here

Asif M., Alvi S.S., Azaz T., Khan A.R., Tiwari B., Hafeez B.B, & Nasibullah M. (2023). Novel Functionalized Spiro [Indoline-3,5′-pyrroline]-2,2′dione Derivatives: Synthesis, Characterization, Drug-Likeness, ADME, and Anticancer Potential. International Journal of Molecular Sciences, 24(8), 7336.

Publication 2023

MMFF94

Derivatives Hydrogens Ligands Molecular force Proteins

Corresponding Organization : The University of Texas Rio Grande Valley

Other organizations : Centre of Biomedical Research, Sanjay Gandhi Post Graduate Institute of Medical Sciences

Top 5 similar protocols

Variable analysis

independent variables

Structural modification
Geometrical correction
Optimization

dependent variables

Three-dimensional structure of synthesized SOX derivatives
Interaction between protein-ligand complexes

control variables

Merck Molecular Force Field (MMFF94) for structural modification, geometrical correction, and optimization
Protoss for predicting hydrogens for protein-ligand interactions
Single-step minimization by the steepest descent method for 500 steps and an RMS gradient of 0.01
Protonation state of ligands at pH 7.4

Annotations

Based on most similar protocols

Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.

As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.

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!