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Article ; Online: An insight into the interaction between α-ketoamide- based inhibitor and coronavirus main protease: A detailed in silico study.

Banerjee, Snehasis

2020 Volume 269, Page(s) 106510

Abstract: The search for therapeutic drugs that can neutralize the effects of COVID-2019 (SARS-CoV-2) infection is the main focus of current research. The coronavirus main protease ( ... ...

Abstract	The search for therapeutic drugs that can neutralize the effects of COVID-2019 (SARS-CoV-2) infection is the main focus of current research. The coronavirus main protease (M
MeSH term(s)	Amides/chemistry ; Amides/metabolism ; Binding Sites ; Catalytic Domain ; Coronavirus/enzymology ; Coronavirus/isolation & purification ; Coronavirus Infections/pathology ; Coronavirus Infections/virology ; Coronavirus M Proteins/antagonists & inhibitors ; Coronavirus M Proteins/metabolism ; Drug Design ; Humans ; Hydrogen Bonding ; Molecular Docking Simulation ; Peptide Hydrolases/chemistry ; Peptide Hydrolases/metabolism ; Protease Inhibitors/chemistry ; Protease Inhibitors/metabolism ; Quantum Theory ; Thermodynamics ; Viral Proteins/antagonists & inhibitors ; Viral Proteins/metabolism
Chemical Substances	Amides ; Coronavirus M Proteins ; M protein, SARS-CoV ; Protease Inhibitors ; Viral Proteins ; Peptide Hydrolases (EC 3.4.-)
Language	English
Publishing date	2020-11-28
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	185052-0
ISSN	1873-4200 ; 0301-4622
ISSN (online)	1873-4200
ISSN	0301-4622
DOI	10.1016/j.bpc.2020.106510
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Book ; Online: An Insight into the Interaction Between α-Ketoamide-Based Inhibitor and Coronavirus Main Protease

Banerjee, Snehasis

A Detailed in Silico Study

2020

Abstract: ... The search for therapeutic drugs that can neutralize the effects of COVID-2019 (SARS-CoV-2) infection is the main focus of current research. The coronavirus main protease (M ... pro ... ) is an attractive target for anti-coronavirus drug design. ...

Abstract	The search for therapeutic drugs that can neutralize the effects of COVID-2019 (SARS-CoV-2) infection is the main focus of current research. The coronavirus main protease (M<sub>pro</sub>) is an attractive target for anti-coronavirus drug design. Further, α-ketoamide is proved to be very effective as a reversible covalent-inhibitor against cysteine proteases. Herein, we report on the non-covalent to the covalent adduct formation mechanism of α‑ketoamide-based inhibitor with the enzyme active site amino acids by QM/SQM model (QM= quantum mechanical, SQM= semi-empirical QM). To uncover the mechanism, we focused on two approaches: a concerted and a stepwise fashion. The concerted pathway proceeds via deprotonation of the thiol of cysteine (here, Cys<sub>145</sub> SgH) and simultaneous reversible nucleophilic attack of sulfur onto the α-ketoamide warhead. In this work, we propose three plausible concerted pathways. On the contrary, in a traditional two-stage pathway, the first step is proton transfer from Cys<sub>145</sub> SgH to His<sub>41</sub> Nd forming an ion pair, and consecutively, in the second step, the thiolate ion attacks the a-keto group to form a thiohemiketal. In this reaction, we find that the stability of the tetrahedral intermediate oxyanion/hydroxyl hole plays an important role. Moreover, as the α-keto group has two faces Si or Re for the nucleophilic attack, we considered both possibilities of attack leading to S- and R-thiohemiketal. We computed the structural, electronic, and energetic parameters of all stationary points including transition states via ONIOM methodology at B3LYP/6-31G(d):PM6 level. Furthermore, to get more accurate results, we also calculated the single-point dispersion-corrected energy profile by using ωB97X-D/6-31G(d,p):PM6 level. Additionally, to characterize covalent, weak noncovalent interaction (NCI) and hydrogen-bonds, we applied NCI-reduced density gradient (NCI-RDG) methods along with Bader’s Quantum Theory of Atoms-in-Molecules (QTAIM) and natural bonding orbital (NBO) analysis.
Keywords	covid19
Publisher	American Chemical Society (ACS)
Publishing country	us
Document type	Book ; Online
DOI	10.26434/chemrxiv.12787463
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: An Insight into the Interaction Between α-Ketoamide-Based Inhibitor and Coronavirus Main Protease

Banerjee, Snehasis

A Detailed in Silico Study

2020

Abstract	The search for therapeutic drugs that can neutralize the effects of COVID-2019 (SARS-CoV-2) infection is the main focus of current research. The coronavirus main protease (M<sub>pro</sub>) is an attractive target for anti-coronavirus drug design. Further, α-ketoamide is proved to be very effective as a reversible covalent-inhibitor against cysteine proteases. Herein, we report on the non-covalent to the covalent adduct formation mechanism of α‑ketoamide-based inhibitor with the enzyme active site amino acids by QM/SQM model (QM= quantum mechanical, SQM= semi-empirical QM). To uncover the mechanism, we focused on two approaches: a concerted and a stepwise fashion. The concerted pathway proceeds via deprotonation of the thiol of cysteine (here, Cys<sub>145</sub> SgH) and simultaneous reversible nucleophilic attack of sulfur onto the α-ketoamide warhead. In this work, we propose three plausible concerted pathways. On the contrary, in a traditional two-stage pathway, the first step is proton transfer from Cys<sub>145</sub> SgH to His<sub>41</sub> Nd forming an ion pair, and consecutively, in the second step, the thiolate ion attacks the a-keto group to form a thiohemiketal. In this reaction, we find that the stability of the tetrahedral intermediate oxyanion/hydroxyl hole plays an important role. Moreover, as the α-keto group has two faces Si or Re for the nucleophilic attack, we considered both possibilities of attack leading to S- and R-thiohemiketal. We computed the structural, electronic, and energetic parameters of all stationary points including transition states via ONIOM methodology at B3LYP/6-31G(d):PM6 level. Furthermore, to get more accurate results, we also calculated the single-point dispersion-corrected energy profile by using ωB97X-D/6-31G(d,p):PM6 level. Additionally, to characterize covalent, weak noncovalent interaction (NCI) and hydrogen-bonds, we applied NCI-reduced density gradient (NCI-RDG) methods along with Bader’s Quantum Theory of Atoms-in-Molecules (QTAIM) and natural bonding orbital (NBO) analysis.
Keywords	covid19
Publisher	American Chemical Society (ACS)
Publishing country	us
Document type	Book ; Online
DOI	10.26434/chemrxiv.12787463.v1
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Application of a distinctly bent, trinuclear, end-to-end azide bridged, mixed valence cobalt(iii/ii/iii) complex in the fabrication of photosensitive Schottky barrier diodes.

Bhunia, Sudip / Das, Mainak / Banerjee, Snehasis / Drew, Michael G B / Ray, Partha Pratim / Chattopadhyay, Shouvik

RSC advances

2024 Volume 14, Issue 16, Page(s) 11185–11196

Abstract: A mixed-valence trinuclear cobalt(iii)-cobalt(ii)-cobalt(iii) complex, [(μ-1,3- ... ...

Abstract	A mixed-valence trinuclear cobalt(iii)-cobalt(ii)-cobalt(iii) complex, [(μ-1,3-N
Language	English
Publishing date	2024-04-08
Publishing country	England
Document type	Journal Article
ISSN	2046-2069
ISSN (online)	2046-2069
DOI	10.1039/d4ra01406e
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Book ; Online: ProxiTrak

Chandel, Vivek / Banerjee, Snehasis / Ghose, Avik

Intelligent Enablement of Social Distancing & Contact Tracing for a Safer Workplace in the New Normal

2022

Abstract: This paper describes an innovative solution that enables the enterprises to bring their associates (or employees) back to physical workspaces for critical operations in a safe manner in the wake of current COVID-19 pandemic. ... Comment: CSI YITPA Region ... ...

Abstract	This paper describes an innovative solution that enables the enterprises to bring their associates (or employees) back to physical workspaces for critical operations in a safe manner in the wake of current COVID-19 pandemic. Comment: CSI YITPA Region II Winning Paper
Keywords	Computer Science - Human-Computer Interaction
Publishing date	2022-08-25
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Effect of Main Versus Ancillary Ligand Substitution on the Photophysical Properties of a Series of Ir(III) Complexes: A Detailed Theoretical Investigation.

Gayen, Pallab / Das, Ujjwal / Banerjee, Snehasis

The journal of physical chemistry. A

2020 Volume 124, Issue 23, Page(s) 4654–4665

Abstract: Herein, we report the effects of different electron-withdrawing groups (EWG) (-F) and electron-donating groups (EDG) (-OMe and - ... ...

Abstract	Herein, we report the effects of different electron-withdrawing groups (EWG) (-F) and electron-donating groups (EDG) (-OMe and -NH
Language	English
Publishing date	2020-06-02
Publishing country	United States
Document type	Journal Article
ISSN	1520-5215
ISSN (online)	1520-5215
DOI	10.1021/acs.jpca.0c03102
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Book ; Online: Talk-to-Resolve

Pramanick, Pradip / Sarkar, Chayan / Banerjee, Snehasis / Bhowmick, Brojeshwar

Combining scene understanding and spatial dialogue to resolve granular task ambiguity for a collocated robot

2021

Abstract: The utility of collocating robots largely depends on the easy and intuitive interaction mechanism with the human. If a robot accepts task instruction in natural language, first, it has to understand the user's intention by decoding the instruction. ... ...

Abstract	The utility of collocating robots largely depends on the easy and intuitive interaction mechanism with the human. If a robot accepts task instruction in natural language, first, it has to understand the user's intention by decoding the instruction. However, while executing the task, the robot may face unforeseeable circumstances due to the variations in the observed scene and therefore requires further user intervention. In this article, we present a system called Talk-to-Resolve (TTR) that enables a robot to initiate a coherent dialogue exchange with the instructor by observing the scene visually to resolve the impasse. Through dialogue, it either finds a cue to move forward in the original plan, an acceptable alternative to the original plan, or affirmation to abort the task altogether. To realize the possible stalemate, we utilize the dense captions of the observed scene and the given instruction jointly to compute the robot's next action. We evaluate our system based on a data set of initial instruction and situational scene pairs. Our system can identify the stalemate and resolve them with appropriate dialogue exchange with 82% accuracy. Additionally, a user study reveals that the questions from our systems are more natural (4.02 on average on a scale of 1 to 5) as compared to a state-of-the-art (3.08 on average). Comment: Accepted in Elsevier Journal of Robotics and Autonomous Systems (RAS)
Keywords	Computer Science - Robotics ; Computer Science - Artificial Intelligence ; Computer Science - Computer Vision and Pattern Recognition
Subject code	004
Publishing date	2021-11-22
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Sequence-Agnostic Multi-Object Navigation

Gireesh, Nandiraju / Agrawal, Ayush / Datta, Ahana / Banerjee, Snehasis / Sridharan, Mohan / Bhowmick, Brojeshwar / Krishna, Madhava

2023

Abstract: The Multi-Object Navigation (MultiON) task requires a robot to localize an instance (each) of multiple object classes. It is a fundamental task for an assistive robot in a home or a factory. Existing methods for MultiON have viewed this as a direct ... ...

Abstract	The Multi-Object Navigation (MultiON) task requires a robot to localize an instance (each) of multiple object classes. It is a fundamental task for an assistive robot in a home or a factory. Existing methods for MultiON have viewed this as a direct extension of Object Navigation (ON), the task of localising an instance of one object class, and are pre-sequenced, i.e., the sequence in which the object classes are to be explored is provided in advance. This is a strong limitation in practical applications characterized by dynamic changes. This paper describes a deep reinforcement learning framework for sequence-agnostic MultiON based on an actor-critic architecture and a suitable reward specification. Our framework leverages past experiences and seeks to reward progress toward individual as well as multiple target object classes. We use photo-realistic scenes from the Gibson benchmark dataset in the AI Habitat 3D simulation environment to experimentally show that our method performs better than a pre-sequenced approach and a state of the art ON method extended to MultiON.
Keywords	Computer Science - Robotics ; Computer Science - Artificial Intelligence ; Computer Science - Machine Learning
Subject code	629
Publishing date	2023-05-10
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Phenoxo-bridged dinuclear mixed valence cobalt(III/II) complexes with reduced Schiff base ligands: synthesis, characterization, band gap measurements and fabrication of Schottky barrier diodes.

Banerjee, Abhisek / Das, Dhananjoy / Ray, Partha Pratim / Banerjee, Snehasis / Chattopadhyay, Shouvik

Dalton transactions (Cambridge, England : 2003)

2021 Volume 50, Issue 5, Page(s) 1721–1732

Abstract: Two homometallic class-I dinuclear mixed valence cobalt complexes, [(N3)CoIIIL1(μ-C6H4(NO2)CO2)CoII(N3)] (1) and [(N3)CoIIIL2(μ-C6H4(NO2)CO2)CoII(N3)] (2), have been synthesized using multisite N2O4 coordination ligands, H2L1 {where H2L1 = (2,2-dimethyl- ... ...

Abstract	Two homometallic class-I dinuclear mixed valence cobalt complexes, [(N3)CoIIIL1(μ-C6H4(NO2)CO2)CoII(N3)] (1) and [(N3)CoIIIL2(μ-C6H4(NO2)CO2)CoII(N3)] (2), have been synthesized using multisite N2O4 coordination ligands, H2L1 {where H2L1 = (2,2-dimethyl-1,3-propanediyl)bis(iminomethylene)bis(6-methoxyphenol) and H2L2 = (2,2-dimethyl-1,3-propanediyl)bis(iminomethylene)bis(6-ethoxyphenol)}. Each complex has been structurally characterized by single crystal X-ray diffraction and spectral analysis. Both the cobalt centers in these dinuclear complexes adopt a distorted-octahedral geometry, where the cobalt(iii) center resides at the inner N2O2 cavity and the cobalt(ii) center resides at the outer O4 cavity of the reduced Schiff base. Both of them show good electrical conductivity, which has been rationalized by band gap measurements. The band gap in the solid state has been determined by experimental and DFT calculations and it confirms that each of the two complexes behaves as a semiconductor. The space-charge-limited current (SCLC) theory is employed to evaluate the charge transport parameters such as effective carrier mobility and transit time for both complexes. The difference in the conductivity values of the complexes may be correlated with the strengths of extended supramolecular interactions in the complexes. Bader's quantum theory of atoms-in-molecules (QTAIM) is applied extensively to get quantitative and qualitative insights into the physical nature of weak non-covalent interactions. In addition, the non-covalent interaction reduced density gradient (NCI-RDG) methods well support the presence of such non-covalent intermolecular interactions.
Language	English
Publishing date	2021-02-08
Publishing country	England
Document type	Journal Article
ZDB-ID	1472887-4
ISSN	1477-9234 ; 1364-5447 ; 0300-9246 ; 1477-9226
ISSN (online)	1477-9234 ; 1364-5447
ISSN	0300-9246 ; 1477-9226
DOI	10.1039/d0dt03707a
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Article ; Online: Two rhodamine-azo based fluorescent probes for recognition of trivalent metal ions: crystal structure elucidation and biological applications.

Mandal, Jayanta / Pal, Kunal / Ghosh Chowdhury, Sougata / Karmakar, Parimal / Panja, Anangamohan / Banerjee, Snehasis / Saha, Amrita

Dalton transactions (Cambridge, England : 2003)

2022 Volume 51, Issue 40, Page(s) 15555–15570

Abstract: Two rhodamine and azo based chemosensors (HL1 = (3',6'-bis(ethylamino)-2-((2-hydroxy-3-methoxy-5-(phenyldiazenyl)benzylidene)amino)-2',7'-dimethylspiro[isoindoline-1,9'-xanthen]-3-one) and HL2 = (3',6'-bis(ethylamino)-2-(((2-hydroxy-3-methoxy-5-( ...

Abstract	Two rhodamine and azo based chemosensors (HL1 = (3',6'-bis(ethylamino)-2-((2-hydroxy-3-methoxy-5-(phenyldiazenyl)benzylidene)amino)-2',7'-dimethylspiro[isoindoline-1,9'-xanthen]-3-one) and HL2 = (3',6'-bis(ethylamino)-2-(((2-hydroxy-3-methoxy-5-(
MeSH term(s)	Aluminum/analysis ; Fluorescent Dyes/chemistry ; Ions/analysis ; Metals ; Optical Imaging ; Rhodamines/chemistry ; Spectrometry, Fluorescence
Chemical Substances	Fluorescent Dyes ; Ions ; Metals ; Rhodamines ; Aluminum (CPD4NFA903)
Language	English
Publishing date	2022-10-18
Publishing country	England
Document type	Journal Article
ZDB-ID	1472887-4
ISSN	1477-9234 ; 1364-5447 ; 0300-9246 ; 1477-9226
ISSN (online)	1477-9234 ; 1364-5447
ISSN	0300-9246 ; 1477-9226
DOI	10.1039/d2dt00399f
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