#DrugDesign

[drugdesignerlife]

CADD Vault

It's an open-source repository dedicated to sharing resources, tools, and knowledge in the field of computer-aided drug design.

You can look here for some resources if you wish.

You can find here websites and github repositories.

[rmcodesblog]

Many of the aspirants had undergone our training for Drug Design and Molecular Docking online courses with a certificate in our institution and became successful professionals in the field. We ensure quality training with good knowledge. We assist the candidates with the necessary study materials.

[magazinesubscriptions11]

Research & Reviews: A Journal of Drug Design & Discovery Journal

Research & critiques: A magazine of Drug layout & Discovery (RRJoDDD) This magazine covers the cutting-edge studies on how pills paintings , rational approaches such as shape based totally drug layout,Molecular processes to optimization of Drug shipping , and includes a wide variety of new Drug advancements.

[royalvoxpost]

Tweeted

#ProteinDesign #DrugDesign #Bioinformatics #AI: scientists have devised a deep learning model to improve the location prediction of zinc ions in protein structures. The model could be used to engineer protein-protein interactions and novel metallodrugs https://t.co/33F8njWKjb https://t.co/IOYGyhrwtc

— The Royal Vox Post (@RoyalVoxPost) May 11, 2023

[jobrxiv]

Postdoctoral Research Associate in Computational Biology University of Edinburgh Application Deadline: 2023-01-27 We are looking for an exceptionally talented and motivated scientist to take up a fully funded position as postdoctoral research associate (PDRA) in computational biology, as part of the EPSRC Early C... See the full job description on jobRxiv: https://jobrxiv.org/job/university-of-edinburgh-27778-postdoctoral-research-associate-in-computational-biology-3/?feed_id=34000 #ScienceJobs #hiring #research #deeplearning #machine #learning #proteins #drugdesign #raredisease

[biodiscovery-group]

WORKSHOP in IMMUNOLOGY & IMMUNOTECHNOLOGY | Live session with Virtual Lab Simulation | Only in ₹ 240 & US $ 5 🤳🤳Video of the session will be recorded and shared with the registered participants. Register from here https://www.townscript.com/e/immunoinformatics-immunotechnology-workshop All upcoming https://www.bdglifesciences.com/courses #envisionwithbdg #itsdifferentbybiodiscovery #bdglifesciences #bioinformatics #biotechnology #bioinformaticscompany #10yearsofexcellence #biodiscoverygroup #onlineteaching #onlinelearning #biotechnologyindustry #admet #onlinebioinformatics #bioinformaticsworkshop #onlinebioinformaticscourse #bioinformaticsonlinetraining #drugdiscovery #drugdesign #immunology #immunoinformatics #immunotechnology https://www.instagram.com/p/CKYvRpEjvgW/?igshid=gjga4vaskq3g

[foodngoodlog-blog]

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[sciencepunchman]

Problems of Structure Based Drug Design and Molecular Docking Softwares

The ultimate docking is to determine the binding probability of two molecules by calculating the geometric shape compatibility and molecular affinity with computer algorithms.

Protein-ligand or protein-protein interaction modelling softwares have been developed over years. Computers have become stronger, different algorithms are made, more complex functions implemented. All of these factors contributed to simulate a real life molecular interaction software. Unfortunately we haven’t achieved yet. 

For the sake of drug discovery, we’ve screened drug candidates and tried to find novel therapeutics in medicine and predict the outcome of the complex molecular interaction. It did give us valuable information but also gave false positive results.

The physiology of the docking software

Docking is all about posing and scoring. Posing means depicting molecular geometric compatibility in a 3D space whereas scoring is to calculate simulative reaction free energy and predicting the binding affinity of the molecules. Docking is more probable if the molecules are geometrically favorable, has negative free energy and high affinity.

The inputs of the docking software are 3D x-ray crystallography or nmr spectroscopy images of interacting molecules and the output is the score function result and final geometric shape.

Of course the crystal image is not how the molecule behaves or does not show its’ all possible configurations. One can say, the crystal image is the snapshot of the molecule.

Prediction of protonation in certain pH environments is one of the most important calculations that the computer must address.

The problems

Imperfect x-ray crystallography or nmr spectroscopy images.

Challenge to differentiate O, N or double bonded carbon atoms in crystallography.

Low density images

Xray structures don’t have information about protonation of O or N atoms.

The challenge of chemistry itself.

The 360 degree rotating nature of single C-C bonds

Tautomerism

Pseudorotation

Unsatisfied hydrogen bonds vs hydrophobicity

Protonation

Limitations of computers

Insufficient computer power to analyze all the conformational changes

Complexity of H2O-water molecules.

Q & A

How does a software deal with some of the problems of imperfect crystallography images, the nature of chemistry and the limitations of computer power?

> You can use prediction tools for most of the situations including rotations, tautomers, protonations, side chain flips or water orientations.

> Crystallography problems might be solved by using multiple crystal structure if available.

> For torsional and rotational problems, you can split the molecule into pieces and try to fit into the pocket. First, the base portion docking construction is optimized and several possible solution are made. The next step is docking the 2nd part of the molecule. Again, several variations are made, but the variations should be continuous with the ligand base. This method is called incremental construction.

> Using triangles for the ligands’ head and tail sites and matching the proteins’ pocket with the donor - acceptor interaction is what the program does. After the possible solutions are found, the RMSD (root mean square deviation, basically a function of atomic distances) is calculated.

> For scoring or estimating the affinity, many different methods are being used. Force fields approach (has too many paramethers to be calculated, dG intermolecular bonds), Quantum mechanics, statistical approach (you must know some real interactions before), HYDE etc. It is a hot topic in bioinformatics.

[eurofinsadvinus]

We offer molecular modeling and computational chemistry services to help advance your drug discovery efforts. Our team has expertise across multiple therapeutic areas. To know more follow the link - https://lnkd.in/eKvx9JP8

[tdevros]

(via 'SMILES' TO STRUCTURE getting creative with elements in drug design.)

[drugdesignerlife]

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9867171/#B257-pharmaceutics-15-00049

The article which introduces the basic aspects of in silico studies in context of drug design.

[rmcodesblog]

Many of the aspirants had undergone our training for Drug Design and Molecular Docking online courses with a certificate in our institution and became successful professionals in the field. We ensure quality training with good knowledge. We assist the candidates with the necessary study materials.

[rajalakshmischoolofbusiness]

Quantitative Structure-Activity Relationship (QSAR) models attempt to relate the structure of the molecule with its chemical and biological activity.

[scraffters]

#scraffterisnk #Attaris #techno

[royalvoxpost]

Tweeted

#Oncology #DrugDesign #Biomarkers: researchers have used several #Bioinformatics tools to identify long non-coding RNAs associated with papillary thyroid cancer (PTC). The approach could help develop new therapeutic strategies for the treatment of PTC - https://t.co/OVDiuZA7Bo https://t.co/tvvO5KBPVL

— The Royal Vox Post (@RoyalVoxPost) Mar 16, 2023