DL COMP BIOTECH

Binding site is a region on a macromolecule such as a protein that binds to another molecule with specificity. Some pockets or concave site can already exist in a ligand-free structure of a protein. Sometimes, a binding site is flat in the absence of a ligand and only forms in the presence of a ligand (i.e., induced fit) or only opens transiently for short periods of time (i.e., conformational selection); such binding sites are called cryptic sites. Cryptic pockets : not easily detectable in the APO state, requires conformational changes to become apparent, and requires a ligand to be detected. These sites can be important for drug discovery because they can provide previously undescribed pockets and thus enable targeting of proteins that would otherwise be considered undruggable. Conventional approaches for cryptic site discovery: experimentally by fragment-based ligand discovery and computationally by long molecular dynamics simulations, fragment docking, identifications of small mol...

 Hi guys,  Here is a latest review article on  Tracing the footsteps of autophagy in computational biology . This review article is an open access article published in Briefings in Bioinformatics. If you are interested to check the latest research on autophagy using the computational biology approaches such as mathematical modelling, artificial intelligence, systems biology, databases, etc. this review is a one stop junction for you. The goal of this review is to show how systems biology approaches are being utilized to examine the autophagy process.  The utilization of computational methods incorporating mathematical modelling and network analysis in the autophagy process is discussed in detail.  This article covers a variety of mathematical models for investigating autophagy that are based on a system of differential equations.  The importance of network analysis and machine learning in identifying the core regulatory gear driving the autophagy process ha...

You'll need the MMTSB toolkit for this tutorial. This is not included in AMBER but is freely available via GitHub. We have discussed how to install it on Linux (Centos 7) in our earlier blog post:  mmtsb-toolset-installation . The following instructions are also provided in AMBER tutorials ( https://ambermd.org/tutorials/basic/tutorial3/section6.htm , which includes scripts and commands for clustering. However, we've provided the quick tour of the steps we took to execute it in our study. In this case, the K-means clustering algorithm is applied, which traverses the pathway in search of clusters of identical structures. It then generates centroids for each cluster and calculates the root mean square deviation (RMSD) of each structure in the trajectory with respect to each cluster. 1. Prepare the directories mkdir clustering cd clustering mkdir PDBfit 2. Use cpptraj to extract multiple PDB's from the trajectory in the clustering folder #first save this script: "extrac...

MMTSB stands for  Multiscale Modeling Tools for Structural Biology.  It is a novel collection of utilities and programming libraries that enable the simulation of proteins and nucleic acids to use advanced sampling and multiscale modelling techniques. For classical all-atom simulations, the tool set interacts with the current molecular modelling packages CHARMM and Amber, and with MONSSTER for lattice-based low-resolution conformational sampling. The tool set is intended for structural biology applications that need the prediction, refining, and/or extended conformational sampling of protein or nucleic acid structures. It also incorporates an ensemble computing capability that enables the control and execution of modelling tasks on a broad range of conformations. For Further details the links are given below. Installation instructions for centos 7: 1. The package is available on GITHUB: https://github.com/mmtsb/toolset #From here download the zip file from the "code" option. ...

UNKNOWN FACTS ABOUT THE MANHATTAN PROJECT: PART 1 The latter years of World War II were defined by a technological arms race and the pursuit of a superweapon capable of subduing the other side. Germany developed a range of technologically powerful "wonder weapons," but the atomic bomb escaped its researchers. On the other hand, the United States deciphered the bomb's secret through the "Manhattan Project," ushering in the first use of atomic weapons in war, the defeat of Japan, and the beginning of a new age of uneasy peace. This was one of the most secret projects of the US and hence was bestowed with flawless security. District officials went above and above to ensure that no one without the required approval was permitted access to site structures or facilities. Each site featured many security checkpoints that were manned twenty-four hours a day, seven days a week by military police. Additionally, each site's perimeter was ringed by thick barbed-wire fen...