DL COMP BIOTECH

Before beginning any homology modelling, verify that the templates in Blastp (protein blast) are suitable for constructing the model for your query sequence using the pdb as the search set.  If you obtain greater than 40% sequence similarity, you can proceed with homology modelling.  If you have Schrodinger, you can use the PRIME homology modelling module in this suite. Otherwise, I-TASSER, SWISS-MODEL, or Phyre2 servers may be used.  Additionally, Modeller can be utilized. It is a self-contained programme. If the sequence similarity of your protein is really low, then try to search with  DELTA-BLAST  (Domain Enhanced Lookup Time Accelerated BLAST) option in BLASTp . It will yield better homology detection. Or you can proceed with threading-based or ab-initio modelling.  Additionally, secondary structure prediction can be performed prior to modelling. This can be accomplished with PSIPRED or JPRED, for example. There are two forms of modelling: single templ...

#here the command measures the distance between two loops (considering the c-alpha atoms in the loop) and prints output in L1-L2.dat. For amber MD trajectory you may try using the following commands in CPPTRAJ: $AMBERHOME/bin/cpptraj >parm pro_solv.prmtop >trajin md-autoimage.nc >rmsd pro @CA,C,O,N,H first mass >distance :135-149@CA :156-166@CA out L1-L2.dat >run Reference: Interplay among Structural Stability, Plasticity, and Energetics Determined by Conformational Attuning of Flexible Loops in PD-1. https://doi.org/10.1021/acs.jcim.0c01080 https://www.researchgate.net/publication/348511593_Interplay_among_Structural_Stability_Plasticity_and_Energetics_Determined_by_Conformational_Attuning_of_Flexible_Loops_in_PD-1

#Web servers for calculation of RMSD values between a ligand poses.  Please note: One pose should be a reference pose and another should be a query pose. PLDbench:  The RMSD value between two molecules can be calculated using PLDbench. There are four modules in this webserver. Single: This module's functionality is limited to calculating RMSD for the 57 complexes utilized in the benchmarking study. Users must submit the docked pose of a ligand that corresponds to one of the 57 PDB-IDs offered in the drop down option in this module. It accepts three file formats: '.pdb', '.mol2', and '.sdf'. Users can choose the type of RMSD they want to compute. Standard heavy-atom RMSD, Hungarian (symmetry-corrected) heavy-atom RMSD, and Minimum-distance heavy-atom RMSD can all be calculated using this module. As a result, the Hungarian (symmetry-corrected) heavy-atom RMSD value is returned by default.  Link for the server:https://webs.iiitd.edu.in/raghava/pldbench/single.p...

Simple life hacks of bygone times: Clock in a candle  Time is a valuable commodity. One can never reclaim the time he has already lived. Since ancient times, time management has been a necessary skill to acquire. Although the art of time management is not everyone's cup of tea, the ever-evolving technology has aided us significantly in accomplishing this feat. In comparison to now, the old days, when technology was still a baby, lacked many conveniences, as managing time could not have been more difficult in the absence of a clock. However, as the proverb 'necessity is the mother of invention' states, our forefathers came up with a simple yet magnificent idea that resulted in the discovery of an alarm clock made entirely of candles. A candle, a few screws, and a metal plate were all they required. Screws were used to denote time intervals. When the candle burns all the way to the first screw, it falls into the metal plate, producing a "clang," and the proces...

 Blog #6 Hi everyone. There is an extremely useful database called "DIA-DB: A Database and Web Server for the Prediction of Diabetes Drugs," which is recently reported in the American Chemical Society's Journal of Chemical Information and Modeling (JCIM). This is the first and open access web server for the prediction of diabetes drugs. It does not require any registrations and the user receives an email with a comprehensive report containing the prediction results.  It employs two distinct approaches: a) 3D shape-based similarity approach for comparison of antidiabetic approved and experimental compounds. b) inverse virtual screening of the input molecules chosen by users: It performs large-scale inverse docking (using Autodock Vina) on a collection of proteins involved in diabetes with the goal of identifying a query compound's possible target. Researchers may also use the DIA-DB to find out whether any of the already-approved or experimental compounds are included ...

Blog#5 ChemProp can be used to estimate the properties of molecules by utilising a Message Passing Neural Network (MPNN). To make predictions, an MPNN must first be trained on a dataset of molecules with known property values. Once trained, the MPNN can be used to predict similar properties in any new molecule. Here is the link:http://chemprop.csail.mit.edu Till now it has provided models for predicting that molecules can inhibit the growth of bacteria ( antibiotic property), 3Cl pro/mpro of sars-cov. The SARS balanced model is for more exhaustive prediction. AMU SARS-CoV-2 in vitro is for the  estimation of probability that molecule with inhibit the virus replication in vitro)

 Blog #4 Novel drug targets and their mechanism of action : In the United States, the European Union, and Japan, 61 novel drugs were FDA approved in 2020.  Therefore, we feel that this would help students to shortlist their dissertation or Ph.D. topics and explore them. The details are mentioned in the link below. https://www.nature.com/articles/d41573-021-00057-z The main reference is: https://www.nature.com/articles/nrd.2016.230

BLOG #3  Hi Guys,           This is a new tutorial on how to simulate a protein-ligand system: basic steps using AMBER. Before we begin, I hope you have read our previous post on AMBER TUTORIAL-1, since I will only be providing additional information with the ligand here, rather than repeating the previous instructions. #To parameterize the ligand file, we start with Antechamber and then parmchck.  These are a series of tools for creating files for organic molecules and some protein metal centers, which can then be read into LEaP. Junmei Wang created the Antechamber suite, which is intended to be used in conjunction with the general AMBER force field (GAFF) (gaff.dat). This is the package's most crucial program. It can convert a variety of files and assign atomic charges and types to them as well. Sqm (or, alternatively, mopac or divcon), atomtype, am1bcc, bondtype, espgen, respgen, and prepgen are among the programs that antechamber runs in respo...

  Blog #2 Hii guys, This is a new blog for researchers looking to publish their work in reputable journals. You can use  JounalFinder:  https://journalfinder.elsevier.com/ Springer Journal Suggester: https://journalsuggester.springer.com/ Taylor and Francis Journal Suggester : https://authorservices.taylorandfrancis.com/publishing-your-research/choosing-a-journal/journal-suggester/ Here you need to e nter the title and abstract of your paper to easily find journals that could be best suited for publishing.  They uses smart search technology and field-of-research-specific vocabularies to match your paper to scientific journals. Thanks. :)