![Dr. Majid Ali](/img/default-banner.jpg)
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Dr. Majid Ali
Пакистан
Добавлен 22 ноя 2015
Molecular Docking Studies, Molecular Dynamic Simulations, Statistical Analysis in Chemistry, Organic Spectroscopy, Medicinal Chemistry, Discovery Studio, Material Studio, and other Chemistry Related Software, and Special Topics in Chemistry
Gaussian Tutorial-2|DFT Calculations of Nanoclusters| #nanotechnology #chemistry @MajidAli2020
Density Functional Theory (DFT) calculation of carbon-doped nanoclusters with metals such as aluminum, iron, cobalt, nickel, and copper can be processed with Gaussian. This tutorial video explains how to perform DFT calculations of different molecules and compounds. #chemistry #computational #analysis #nanoscience @MajidAli2020
Просмотров: 1 466
Видео
Gaussian tutorial-1|Structure Builder| #computational #chemistry @MajidAli2020
Просмотров 8386 месяцев назад
This tutorial describes how to build structures, fragments, compounds, and files in Gaussian for theoretical studies like DFTs and other calculations through computational means. This software is used for different studies we will explain in our next videos. #chemistry #computational #bioinformatics #theory #analysis @MajidAli2020
Cofactor Part-2|TM-Align|Gene Ontology|Homology|Binding Sites|Molecular Functions #bioinformatics
Просмотров 1827 месяцев назад
Structure-based function prediction through online server COFACTOR part-2 is here which describes how we get our results and what important domain it covers such as protein alignment, gene ontology, homology modeling, active and binding sites, cellular process and molecular functions #chemistry #biochemistry #server @MajidAli2020
Protein Structure-based Function Prediction|Cofactor Zhong Lab Server #bioinformatics #biochemistry
Просмотров 1997 месяцев назад
COFACTOR is an online web server from Zhong Lab a project of the University of Michigan US. It predicts the structure-based function of a polypeptide protein and performs its proper 3D folding from amino acid sequence.
Fusion & Folding of Protein/Enzyme|3D Folding|Phyre2|I-TASSER|EsyPred3D Server #bioinformatics
Просмотров 2847 месяцев назад
Linking, joining and Fusion of two or more proteins, polypeptides, or enzymes are important in Biochemical processes and metabolism. Proteins fusion at genetic level or in-vitro can be processed at computational level by designing proper 3D model and folding of proteins or enzymes after joining with each other which are not already present in databases like PDB and SWISSPROT. Therefore 3D foldi...
t-Test Analysis|Significance b/w Control & Treated|Graphpad Prism #analysis #chemistry #data
Просмотров 2757 месяцев назад
T-test analysis represents data significance between control and treated values in various in-vitro and in-vivo experiments where p-value is threshold value for significance. @MajidAli2020
Statistics|Row Data Mean|Standard Error Mean|SEM|Deviation|SD|Graph|Prism|Analysis #statistics #data
Просмотров 1,6 тыс.7 месяцев назад
Row statistics tool on Graphpad prism software that analyzes data with replicates into mean and standard deviation (SD) and standard error of mean (SEM) making bar graph and data point graph with different groups and values on XY column @Dr. Majid Ali
Geometry of metal complexes|Discovery Studio Visualizer #chemistry #discovery #studio @MajidAli2020
Просмотров 808Год назад
Metal complexes geometry and hybridization, XYZ coordinates, atom attributes, partial charges, oxidation state, etc can be observed through the discovery studio visualizer #complexes #metals @MajidAli2020
Biotransformer Metabolism Prediction Online Web Server #pharmacy #chemistry @MajidAli2020
Просмотров 658Год назад
Biotransformer version 3.0 is an online available web server/tool that can be used to predict metabolism for our compounds/medicines/drugs in the field of pharmacokinetics and medicinal chemistry. It indicates Cyp450 metabolism, phase II metabolism like acylation, glucuronidation, and human gut microbial metabolism, environmental and abiotic metabolism. #medicinal #biochemistry @MajidAli2020
Materials Explorer|Crystal Structure|Graphene|Gaussian|Materials studio|DFT #material @MajidAli2020
Просмотров 2 тыс.Год назад
How can crystal structures be obtained from different materials, compounds, and salts using material explorer and pubChem tools for DFT calculations, energy minimization, and adsorption studies using Gaussian and Material Studio software? #chemistry #crystals @MajidAli2020
Toxicity Estimation Software|LD50|Mutagenicity|surface tension|viscosity|conductivity@MajidAli2020
Просмотров 1,8 тыс.Год назад
TEST software, a toxicity estimation tool is used to predict oral rat LD50 i.e. lethal dose, mutagenicity, developmental toxicity, fathead minnow LC50, bioaccumulation factor, boiling point, melting point, thermal conductivity, surface tension, density, flash point, viscosity and many other descriptors, #pharmacy #medicinal #biochemistry #environment #chemistry @MajidAli2020
Druglikeness|Physicochemical properties|Pharmacokinetics|Toxicity #drug #property @MajidAli2020
Просмотров 1,6 тыс.Год назад
Drug-likeness of the compounds can be predicted or measured through molecular descriptors/physicochemical properties of molecules/drugs, pharmacokinetics/ADME profile, and toxicity of drugs by using different software and online web servers such as molinspiration, preADME, SwissADME and TEST (toxicity estimation software tool) #chemistry #pharmacy #medicinal #biochemistry #drugdiscovery #molecu...
Adsorption Studies by Material Studio #adsorption #material #studio @MajidAli2020
Просмотров 7 тыс.Год назад
adsorption locator tool in material studio is helpful in calculating different type of interactions between substrate of different material like silica, alumina, glass, zeolite and metal oxides and adsorbate such as dyes, paints, chemicals and heavy metals. We can run energy minimization, geometery optimization and simulated annealing with cutoff distance and energy @MajidAli2020
RMSD (Root Mean Square Deviation) Calculation by Discovery Studio Visualizer @MajidAli2020
Просмотров 10 тыс.Год назад
How to calculate RMSD value in Angstrom by using Discovery Studio Visualizer after molecular docking of co-crystallized ligand into the active site of target by using MOE (Molecular Operating Environment) or other softwares like Autodock etc. #pharmacy #docking @MajidAli2020
An easy way to Import complicated structures to Gaussian from ChemDraw & Discovery Studio Visualizer
Просмотров 3,5 тыс.Год назад
How to import complicated or larger structures from ChemDraw, MS Word or DSV? if we dont want to make it in Gaussian and have to run calculations like DFT, minimization or HOMO, LUMO studies. Different file formats such as SDF, Mol, Sybyl Mol2 and gfp can be imported after check, clean and minimize our ligand/structure/compound in ChemDraw and discovery studio visualizer. #chemistry #discovery ...
How to Design, Synthesize Structural Analogues, SAR, X-Ray Crystallography, MD & ADMET of Drug
Просмотров 632Год назад
How to Design, Synthesize Structural Analogues, SAR, X-Ray Crystallography, MD & ADMET of Drug
Drug Design Discovery & Development|Medicinal Chemistry Lect. #medicinal #chemistry @MajidAli2020
Просмотров 582Год назад
Drug Design Discovery & Development|Medicinal Chemistry Lect. #medicinal #chemistry @MajidAli2020
Antibiotics|Classes|Action|Medicnal Chemistry @MajidAli2020 #chemistry #pharmacy #biochemistry
Просмотров 231Год назад
Antibiotics|Classes|Action|Medicnal Chemistry @MajidAli2020 #chemistry #pharmacy #biochemistry
Gibb's Free Energy|Enthalpy|Entropy|Redox Potential|Ligand-Target Interaction @MajidAli2020
Просмотров 278Год назад
Gibb's Free Energy|Enthalpy|Entropy|Redox Potential|Ligand-Target Interaction @MajidAli2020
Analgesics - Narcotics (opioids) & NSAIDs |Medicinal Chem Lect.9 #chemistry #pharmacy @MajidAli2020
Просмотров 336Год назад
Analgesics - Narcotics (opioids) & NSAIDs |Medicinal Chem Lect.9 #chemistry #pharmacy @MajidAli2020
Ligands & Receptors Part 2|Signaling & Response|Medicinal Chem. #medicinal #chemistry @MajidAli2020
Просмотров 389Год назад
Ligands & Receptors Part 2|Signaling & Response|Medicinal Chem. #medicinal #chemistry @MajidAli2020
Medicinal Chemistry| Ligands & Receptors| Signaling & Response #chemistry #pharmacy @MajidAli2020
Просмотров 431Год назад
Medicinal Chemistry| Ligands & Receptors| Signaling & Response #chemistry #pharmacy @MajidAli2020
Inflammation, Allergies & Antihistamines|H1 & H2 Antagonists #medicinal #pharmacy @MajidAli2020
Просмотров 258Год назад
Inflammation, Allergies & Antihistamines|H1 & H2 Antagonists #medicinal #pharmacy @MajidAli2020
Mechanism of Respiratory Drug Action |Antitussive|Branchodilators|Asthma|COPD|Expectorants #pharmacy
Просмотров 384Год назад
Mechanism of Respiratory Drug Action |Antitussive|Branchodilators|Asthma|COPD|Expectorants #pharmacy
Pharmacokinetics(ADMET)|Routes of Drug Administration| Physicochemical properties| Medicinal Chem.5
Просмотров 357Год назад
Pharmacokinetics(ADMET)|Routes of Drug Administration| Physicochemical properties| Medicinal Chem.5
Types & Actions of Drugs|Medicinal Chemistry-4|#medicinal #chemistry #drugdiscovery @MajidAli2020
Просмотров 330Год назад
Types & Actions of Drugs|Medicinal Chemistry-4|#medicinal #chemistry #drugdiscovery @MajidAli2020
Medicinal Chemistry 3 - Sources & Classification of Drugs #chemistry #medicinal @MajidAli2020
Просмотров 387Год назад
Medicinal Chemistry 3 - Sources & Classification of Drugs #chemistry #medicinal @MajidAli2020
Medicinal Chemistry 2 -Pharmacodynamics/Mechanism of Drug Action #chemistry #pharmacy @MajidAli2020
Просмотров 705Год назад
Medicinal Chemistry 2 -Pharmacodynamics/Mechanism of Drug Action #chemistry #pharmacy @MajidAli2020
Medicinal Chemistry 1 - Drug Design & Discovery Process #medicinal #chemistry @MajidAli2020
Просмотров 1,1 тыс.Год назад
Medicinal Chemistry 1 - Drug Design & Discovery Process #medicinal #chemistry @MajidAli2020
Materials Studio - Carbon Nanotubes CNTs & Adsorption of compound/dyes #nanomaterials @MajidAli2020
Просмотров 5 тыс.Год назад
Materials Studio - Carbon Nanotubes CNTs & Adsorption of compound/dyes #nanomaterials @MajidAli2020
nice work. Sir.. please share downloading link..
How to get this software?
Sir, What to do? If my target is not protei or enzyme. My target is Lipid II and Lipid I? How to predict the activity
Sir, What to do? If my target is not protei or enzyme. My target is Lipid II and Lipid I? How to predict the activity
how did you run MOE?
sir how we select the compound as we have much more in the result after MOE docking?
thank you, very useful and well explained!
جزاكم الله خيرا اخي الكريم ❤😂
Sir I am using 2020 version. When I click on "more" then in cell optimization it shows four options none, full, fixed volume and fixed shape. which one I have to select?
Great video
Hello Sir, I want to make a molecular dynamic simulation of Antibiotics on Activated carbon. Do I need to use graphene sheet? Please let me know sir.
No, graphene sheet is different
Thank you, Sir, for sharing your knowledge. I got this message when I tried to run CASTEP on Windows: "Can't create a job for the server: CASTEP. This computer was unable to communicate with the computer providing the server" How do I rectify this error?
Great sir
Sir but in complex ligand is not visible in imod web server
Thanks
Thank you sir✨ It was very useful for me✨✨
How can you perform desorption studies in this??
Please is this software free ?
Sir can u plz make a video on absorption of co2?
I have a problem when i simulate adsorption located of Congo red in Kaolin I have as message: the results are far
🖐️🖐️🖐️
Aoa sir, do u have any contact number? I need guidance plz
Sir, do u have any contact number?
03328503801
sir is not simulation ..i do not show the intreaction between drug and protien its only shows deformity in protein...
merci beaucoup
Sir can you please make vedio on how to plot mtt assay data for 24hrs and 48hrs and calculate p values by comparing to control
Congratulations on your work, which reflects outstanding knowledge and skills. I am particularly interested in the relationship between the position of the sulphonamide functionality and the type of formaldehyde derivative used in constructing the tail of these compounds. Why didn't you explore this further?
Ok nice
How to calculate p value? Please suggest
👍❤️✨
Nicely explained Thanks for the video sir
do you have any materials how to use canter for reaction modeling using ds3 material studio
Sir have you done phonon calculations with MS
How to make √3 × √3 surface model of any matel
What are those scores?
Which one?
@@MajidAli2020 the scores which came in the compound results
Through virtual screening from databases
No sir, I mean the scores which you are saying as similarity scores. What is it's significance?
The higher the score more will be the similarity
hello where can I find that paper
Which paper do u want
Hello sir, how we can added force field in material studio, for example i have interface force field and i want to added this force field in material studio thank you so much
Zabardast sir 🎉
Hello Dr. I want to make a molecular dynamic simulation of H2S on Activated carbon. regarding the activated carbon. do I need to use graphene sheet?
@Dr. Majid Ali I am getting problem to calculate RMSD. kindly help me to solve this problem. Heavy Atom RMSD to All Name Reference RMSD (A) 1KZN 1 1KZN 1 0.0000 output_a_3_model_0 2 output_a_3_model_0 2 0.0000 The following molecule(s) failed due to element types not matching the reference ligand. output_a_3_model_0 2 The order of the atoms has to be the same. Use the Hierarchy View and expand both the reference ligand and the pose to verify that the atoms are listed in the same order.
Salam Alaikum, I am looking for a reference to read more about all the parameters that we need to analyze while docking ligand protein
Is it 2D or 3D structure, how to make conventional cell or primitive cell from it?
Hello, I want to use solvent, for example absorption of K from KCl solution by Al2O3 or zeolite, what I should to do
السلام عليكم كيف افعل هذا البرنامج
Hey. What are the criteria followed to choose the right U and V values? Also, the thickness especially while investigating adsorption following geometry optimization technique.
Find in literature
Dr I have an error in material studio i dont know what to do , i want to calculate absorption of an organic material on the specific atom in the structure of nanotube but it errors , what should i do?
When u take refine adsorption in simple computer it gives problem or may have some other setting issue
hi, I applied for LaCoO3 but got error as "The model contains particles that have not been assigned a forcefield type or The bond increment charging engine has failed to calculate charges for 480 particles" There are missing or unknown forcefield types. how to solve this issue?
❤❤❤
Please Dr .Majid Do you have whatsapp I want to communicate to you necessary??
can i have yours Email sir i want to talk with you
but dear dr why the ligand do not appear !!
It appears look in part 2
Can i plot rmsd using the data i get ?
and how can i get a vedio for my simulation