The amino acid sequences of the human α3 (NP_000734) and β4 (NP_000741) nAChR subunits and the crystal structure of the human α4β2 nAChR (PDBID: 5kxi; Chain A: α4; Chain B: β2; Chain C: β2; Chain D: α4; Chain E: β2) were downloaded from the NCBI website. Using Clustal Omega (https://www.ebi.ac.uk/Tools/msa/ clustalo/), the α3 sequence was aligned with the α4 sequence (Chain A) from the crystal structure, and the β4 sequence was aligned with the β2 sequence (Chain B) from the crystal structure. The unaligned regions of the α3 and β4 subunits (mainly the signal peptide and the M3-M4 intracellular loop) were removed. The homology models of all five chains were built with ICM Pro 1.7 (MolSoft, San Diego, CA, USA; Chain A: α3; Chain B: β4; Chain C: β4; Chain D: α3; Chain E: β4). Five model chains were combined to form a pentameric structure. The receptor was further converted to an ICM object, and energy was minimized using MolMechanics function in ICM Pro. The cocaine molecule was built from the crystal structure, with a PDBID of 2pgz. The docking was performed using ICM Pro with a docking space manually adjusted to cover the transmembrane domain of the receptor. The top-scored pose was used for presentation using Discovery Studio 4.0 Visualizer (BIOVIA, San Diego, CA, USA).
Discovery studio 4.0 visualizer
Manufactured by Dassault Systèmes
Sourced in United States
Discovery Studio 4.0 Visualizer is a software application developed by Dassault Systèmes. It provides a platform for visualizing and analyzing molecular structures and related data. The software offers tools for tasks such as molecular modeling, protein structure prediction, and drug discovery.
Automatically generated - may contain errors
Lab products found in correlation
15 protocols using discovery studio 4.0 visualizer
1
Homology Modeling and Docking of Human nAChR Subunits
2
Molecular Docking of YD Compound
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Molecular docking simulation was carried out using the SYBYL-X2.1.1 (Tripos, St. Louis, MO, USA) with Surflex-Dock Geom mode. The chemical structure of YD was prepared in a mol2 format, and the ligand was docked into chain A of the human NNMT downloaded from the PDB (PDB: 3ROD ). Staged minimization was performed using Powell’s method until the gradient converged to a value of 0.001 kcal/mol·Å. An MMFF94 force field was used with MMFF94 charges. Protomol was generated based on the location of the original ligands, SAH and NCA, with a threshold of 0.5 Å and bloat of 6 Å. The protein movement option was used to allow flexibility in the binding pocket of the protein. Docking performance was validated based on the docking scores, visual inspection, and root-mean-square deviation (RMSD) values of the re-docked poses compared with the original structure. Molecular interactions between the ligand and protein were further analyzed using the Discovery studio 4.0 Visualizer (Biovia, San Diego, CA, USA) or PyMOL-v1.0 (Schrödinger KK, Tokyo, Japan).
3
Molecular Docking of C-K and Annexin A2
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Molecular docking was performed with C-K and Annexin A2 with structure resource of PubChem CID: 9852086 from the NCBI PubChem Compound database (http://www.ncbi.nlm.nih.gov/pccompound ) and PDB ID: 2HYU from the RCSB Protein Data Bank (http://www.rcsb.org/pdb ). Molecular docking was performed with AutoDock tools (version 4.2.6) and visualized with the Discovery Studio 4.0 Visualizer (BIOVIA, CA, USA).
4
Virtual Screening of Protein Complexes
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Virtual screening was conducted using the software AutoDock (version 4.2.6) based on Lamarckian Genetic Algorithm (Scripps Research Institute, La Jolla, CA, USA) according to the manual handbook and other publications. This software uses a sophisticated gradient optimization method in its local optimization procedure. The target used in our study was the crystal structures of HSA and BSA from the Research Collaboratory for Structural Bioinformatics Protein Data Bank (http://www.rcsb.org/pdb ). The predicted complexes were optimized and ranked according to the empirical scoring function, Screen Score, which estimates the binding free energy of the ligand–receptor complex. The most stable distinguished conformation with the minimal binding energy was shown using Discovery Studio 4.0 Visualizer (BIOVIA, CA, USA).
5
Molecular Docking of (20S) G-Rh2 with HSP90
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
We downloaded the crystal structure of HSP90A_N (PDB ID: 4BQG) and HSP90A_MC (PDB ID: 3Q6M) from the RCSB Protein Data Bank (http://www.rcsb.org/pdb , accessed on 11 November 2021). We downloaded the three-dimensional structure of (20S) G-Rh2 (PubChem CID: 119307) from the NCBI PubChem Compound database (http://www.ncbi.nlm.nih.gov/pccompound , accessed on 11 November 2021). The structure of (20S) G-Rh2 was optimized by Chem3D (version 16.0, PerkinElmer, Waltham, MA, USA) to minimize its energy. Then, we performed molecular docking with AutoDock tools (version 4.2.6) with the default setting, based on the Lamarckian genetic algorithm (Scripps Research Institute, La Jolla, CA, USA). Results were optimized according to the empirical scoring function, which estimates the binding free energy of the predicted ligand–receptor complex, and shown by Discovery Studio 4.0 Visualizer (BIOVIA, Paris, France).
6
Molecular Docking of SsD with FTO
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The three-dimensional structure of SsD (PubChem CID:119307) was obtained from the NCBI Pubchem Compound database (http://www.ncbi.nlm.nih.gov/pccompound ) by ChemDraw software, and the crystal structure of FTO (PDB ID: 2HYU6AKW) was obtained from the RCSB Protein Data Bank (http:// www.rcsb.org/pdb). Molecular docking was performed using AutoDock tools (version 4.2.6) at the default setting, based on the Lamarckian Genetic Algorithm (Scripps Research Institute, La Jolla, CA, USA). Hydrogens were added and all H2O2 molecules were removed using the Protein Preparation Wizard in Maestro v9.2. Then, the structure was energy-minimized. The chemical structure of SsD was prepared using LigPrep v2.5, then AMSOL partial atomic charges were assigned. The program Glide v5.7 was used for ligand docking. Flexible Docking was performed with extra precision mode. The number of poses per ligand was set to 10 in post-docking minimization and the best 5 poses were output. The other parameters were kept as default. The molecular structures were generated using PyMOL 1.6.x. We processed the optimum structure of the complex with the Discovery Studio 4.0 Visualizer (BIOVIA, San Diego, CA, USA).
7
Homology Modeling of Human α7nAChR Subunit
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The homology model of the human α7nAChR subunit was made with ICM Pro 3.7–2C (MolSoft, San Diego, CA) using chain A of the EM structure of Torpedo nicotinic receptor (PDBID: 2BG9 chain A) as the template for Fig 1 . The resulting models were used to map the SNPs in the 3D structure using Discovery Studio 4.0 Visualizer (Biovia, San Diego, CA). The same software was also used to present the crystal structures of acetylcholine binding protein (AChBP) with ACh or nicotine in the binding pocket (PDBID: ACh binding with AChBP: 3WIP, nicotine binding with AChBP: 1UW6).
8
Molecular Docking of G-Rh2 and ETC Complexes
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Molecular docking analyses were performed for G-Rh2 and the ETC complexes. Data on the structures of ETC complexes were obtained from the RCSB Protein Data Bank (PDB; http://www.rcsb.org/pdb ), including ETC complex I (PDB ID: 4G73) (27 (link)), ETC complex III (PDB ID: 4PD4) (28 (link)) and ETC complex V (1BMF) (29 (link),30 (link)). Molecular docking was performed with AutoDock tools (version 4.2.6) and visualized with the Discovery Studio 4.0 Visualizer (BIOVIA).
9
Molecular Docking Analysis of AXL Receptor Ligands
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Molecular docking analysis was implemented using the Surflex-Dock module in Sybyl-X2.2.1 (Tripos Inc, St Louis, MO, USA) with the known crystal structure of AXL complexed with ligands (PDB ID: 5U6B). To prepare the protein, hydrogen was added and energy was minimized using Powell's method with the Tripos force field until the root-mean-square derivation (RMSD) values were < 0.05 Kcal/mol·Å. Initial optimization and termination of minimization were set as simplex and gradient, respectively. The new ligands were prepared using Chem3D (PerkinElmer, Waltham, MA, USA). Molecular docking simulations were conducted using the Surflex-Dock mode with the extraction of the original ligand. To generate the active site, a threshold of 0.5 Å and bloat of 0 Å were applied based on the original ligand in the crystal structure. Other parameters were used as default. The results of the docking simulation were validated by comparing the redocked structure to the original pose of the ligand. Molecular interactions between proteins and ligands were further analyzed using Discovery Studio 4.0 Visualizer (BIOVIA, San Diego, CA, USA).
10
Molecular Docking of (20S)G-Rh2 and Annexin A2
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
We downloaded the three-dimensional structure of (20S)G-Rh2 (PubChem CID: 119307) from the NCBI Pubchem Compound database (http://www.ncbi.nlm.nih.gov/pccompound ), and we downloaded the crystal structure of Annexin A2 (PDB ID: 2HYU) from the RCSB Protein Data Bank (http://www.rcsb.org/pdb ). We performed molecular docking with AutoDock tools (version 4.2.6) with the default setting, based on the Lamarckian Genetic Algorithm (Scripps Research Institute, La Jolla, CA, USA). We processed the optimum structure of the complex with the Discovery Studio 4.0 Visualizer (BIOVIA, CA, USA).
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!