Spectral gap optimization of order parameters (SGOOP) [P. Tiwary and B. J. Berne, Proc. Natl. Acad. Sci. U. S. A. 113, 2839 (2016)] is a method for constructing the reaction coordinate (RC) in molecular systems, especially when they are plagued with hard to sample rare events, given larger dictionary or basis functions limited static dynamic information about system. In its original formulation, SGOOP designed construct 1-dimensional RC. Here we extend scope by introducing simple but...

Understanding ligand dissociation mechanisms at an atomic resolution is a highly desired but difficult to achieve objective in experiments as well computer simulations. Structural details of the process are general hard capture experiments, while relevant time scales far beyond molecular dynamics (MD) simulations even with most powerful supercomputers. As such, many different specialized enhanced sampling methods have been proposed that make it possible efficiently calculate protein-ligand...

Separation and sorting of pristine carbon nanotubes (CNTs) from bundle geometry is a very challenging task due to the insoluble nondispersive nature CNTs in aqueous medium. Recently, many studies have been performed address this problem using various organic inorganic solutions, surfactant molecules, biomolecules as dispersing agents. Recent experimental reported DNA be highly efficient geometry. However, there no microscopic study also quantitative estimation dispersion efficiency DNA....

Using all atomistic molecular dynamics (MD) simulations we report the microscopic picture of nanotube-dendrimer complex for PAMAM dendrimer generation 2 to 4 and carbon nanotube chirality (6,5). We find compact wrapping conformations onto surface three generations dendrimer. The degree is more non-protonated compared protonated For comparison also study interaction another dendrimer, poly(propyl ether imine) (PETIM), with show that interacts strongly as PETIM evident from distance closest...

Various unique physical, chemical, mechanical and electronic properties of carbon nanotube (CNT) make it very useful materials for diverse potential application in many fields. Experimentally synthesized CNTs are generally found bundle geometry with a mixture different chirality present challenge to separate them. In this paper we have proposed the PAMAM dendrimer be an ideal candidate separation. To estimate efficiency dispersion from geometry, calculated mean forces (PMF). Our PMF study...

In recent times, computational methods played an important role in the down selection of chemical compounds, which could be a potential drug candidate with high affinity to target proteins. However, screening methodologies, including docking, often fails identify most effective compound, ligand for protein. To solve that, here we have integrated meta-dynamics, enhanced sampling molecular simulation method, all-atom dynamics determine specific compound that main protease novel severe acute...

Since the onset of global pandemic, most focused research currently in progress is development potential drug candidates and clinical trials existing FDA approved drugs for other relevant diseases, order to repurpose them COVID-19. At same time, several high throughput screenings have been reported inhibit viral components during early course infection but with little proven efficacies. Here, we investigate repurposing strategies counteract coronavirus which involves targetable host proteins...

Actin is a major cytoskeletal system that mediates the intricate organization of macromolecules within cells. The bacterial protein MreB prokaryotic actin-like governing cell shape and intracellular in many rod-shaped bacteria, including pathogens. stands as target for antibiotic development, compounds like A22 its analogue, MP265, are identified potent inhibitors MreB. actin shares structural homology with eukaryotic despite lacking sequence similarity. It currently not clear whether small...

Wrapping of mannose-attached PETIM dendrimers around metallic SWNTs<italic>via</italic>non-covalent and van der Waals interactions leads to a large band gap opening.

Abstract The emergence of pandemic situations originated from severe acute respiratory syndrome (SARS)‐CoV‐2 and its new variants created worldwide medical emergencies. Due to the non‐availability efficient drugs vaccines at these emergency hours, repurposing existing can effectively treat patients critically infected by SARS‐CoV‐2. Finding a suitable drug with inhibitory efficacy host‐protein is challenging. A detailed mechanistic understanding kinetics, (dis)association pathways, key...

Abstract Obtaining atomistic resolution of ligand dissociation from a protein is much sought after experimental and computational challenge. Structural details the process are in general hard to capture experiments, while relevant timescales far beyond molecular dynamics (MD) simulations even with most powerful super-computers. As such many different specialized enhanced sampling methods have been proposed that make it possible efficiently calculate mechanisms protein-ligand systems....

Since the onset of global pandemic, most focused research currently in progress is development vaccine candidates and clinical trials existing FDA approved drugs for other relevant diseases, order to repurpose them COVID-19. Here, we investigate drug repurposing strategies counteract coronavirus infection which involves several potential targetable host proteins involved viral replication disease progression. We report high throughput analysis literature-derived that can be used target...

Biological nanopores provide optimum dimensions and an optimal environment to study early aggregation kinetics of charged polyaromatic molecules in the nano-confined regime. It is expected that probing stages nucleation will enable us design a strategy for supramolecular assembly biocrystallization processes. Specifically, we have studied translocation dynamics coronene perylene based salts, through α-hemolysin (α-HL) protein nanopore. The characteristic blocking events time-series signal...

ABSTRACT Actin is a major cytoskeletal system that mediates the intricate organization of macromolecules within cells. The bacterial protein MreB prokaryotic actin-like governing cell shape and intracellular in many rod-shaped bacteria including pathogens. stands as target for antibiotic development, compounds like A22 its analogue, MP265, are identified potent inhibitors MreB. actin shares structural homology with eukaryotic actin, despite lacking sequence similarity. It currently not clear...

Abstract The Epstein-Barr virus (EBV) is one of the cancer-causing gamma type viruses. Although more than 99% people are infected by this at some point, it remains in body a latent state, typically causing only minor symptoms. Our current understanding that known transcription factor (TF), ZTA protein, binds with dsDNA (double stranded deoxyribonucleic acid) and plays crucial role mediating viral latent-to-lytic cycle through binding specific responsive elements (ZREs). However, there no...

The present study aims to develop a paradigm for parcel level horticultural crop identification and web based geospatial information generation using high resolution satellite data open source GIS software. Initially get the spectral differences among crops both visual as well digital classifications were performed particularly number band ratios generated. Based on obtained NDVI values classes categorized then matched with plot GPS survey including farmers information. achieved...

Spectral gap optimization of order parameters (SGOOP) (Tiwary and Berne, Proc. Natl. Acad. Sci. 113 2839 (2016)) is a method for constructing the reaction coordinate (RC) in molecular systems, especially when they are plagued with hard to sample rare events, given larger dictionary or basis functions, limited static dynamic information about system. In its original formulation, SGOOP designed construct 1-dimensional RC. Here we extend scope by introducing simple but powerful extension based...

Here we report new chemical entities that are highly specific in binding towards the 3-chymotrypsin- like cysteine protease (3CLpro) protein present novel SARS-CoV2 virus. The viral 3CLproprotein controls coronavirus replication. Therefore, 3CLpro is identified as a target for drug molecules. We have implemented an enhanced sampling method combination with molecular dynamics and docking to bring down computational screening search space four molecules could be synthesised tested against...

Exploring structural behavior of pure 1-palmitoyl-2-stearoyl-sn-glycero-3-phosphocholine (PSPC) and multicomponent PSPC 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N[amino(poly(ethylene glycol))-2000] (DSPE-PEG2000) membranes their interaction with pharmaceutically important drugs carry huge importance in drug delivery. Using all-atom molecular dynamics (MD) simulations, we investigated the phase PEGylated at temperature range 280–360 K. We observe a gel-to-liquid crystalline transition...

Here we report new chemical entities that are highly specific in binding towards the 3-chymotrypsin- like cysteine protease (3CLpro) protein present novel SARS-CoV2 virus. The viral 3CLproprotein controls coronavirus replication. Therefore, 3CLpro is identified as a target for drug molecules. We have implemented an enhanced sampling method combination with molecular dynamics and docking to bring down computational screening search space four molecules could be synthesised tested against...

&lt;p&gt;Here, we report new chemical entities that exhibit highly specific binding to the 3-chymotrypsin-like cysteine protease (3CLpro) present in novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Because viral 3CLpro protein controls replication, is identified as a target for drug molecules. We implemented an enhanced sampling method combination with molecular dynamics and docking reduce computational screening search space four molecules could be synthesized tested...

Here, we report new chemical entities that exhibit highly specific binding to the 3-chymotrypsin-like cysteine protease (3CLpro) present in novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Because viral 3CLpro protein controls replication, is identified as a target for drug molecules. We implemented an enhanced sampling method combination with molecular dynamics and docking reduce computational screening search space four molecules could be synthesized tested against...