P. Kar

发表

PRIMO: A Transferable Coarse-grained Force Field for Proteins.

M. Feig, S. M. Gopal, Yi-Ming Cheng, 2013, Journal of chemical theory and computation.

Recent advances in transferable coarse-grained modeling of proteins.

M. Feig, P. Kar, 2014, Advances in protein chemistry and structural biology.

Theoretical mimicry of biomembranes

S. Höfinger, Thomas Weidemann, P. Kar, 2009, FEBS letters.

Comparing Semi-Empirical versus Classic Charge Assignments in BioMolecules and their Effect on Electrostatic Potentials

S. Mohanty, U. Hansmann, J. Meinke, 2007 .

Importance of polar solvation and configurational entropy for design of antiretroviral drugs targeting HIV-1 protease.

R. Lipowsky, V. Knecht, P. Kar, 2013, The journal of physical chemistry. B.

Exploring the energetic basis of binding of currently used drugs against HIV-1 subtype CRF01_AE protease via molecular dynamics simulations

P. Kar, Md Fulbabu Sk, N. A. Jonniya, 2020, Journal of biomolecular structure & dynamics.

Investigating the mechanism of recognition and structural dynamics of nucleoprotein-RNA complex from Peste des petits ruminants virus via Gaussian accelerated molecular dynamics simulations

Sayan Poddar, D. Nayak, P. Kar, 2020, Journal of biomolecular structure & dynamics.

Computational Investigation of Structural Dynamics of SARS-CoV-2 Methyltransferase-Stimulatory Factor Heterodimer nsp16/nsp10 Bound to the Cofactor SAM

Sayan Poddar, P. Kar, Md Fulbabu Sk, 2020, Frontiers in Molecular Biosciences.

Investigating Conformational Dynamics of Lewis Y Oligosaccharides and Elucidating Blood Group Dependency of Cholera Using Molecular Dynamics

P. Kar, B. Ghosh, R. Roy, 2020, ACS omega.

Plant-derived natural polyphenols as potential antiviral drugs against SARS-CoV-2 via RNA‐dependent RNA polymerase (RdRp) inhibition: an in-silico analysis

A. Sonawane, P. Kar, Md Fulbabu Sk, 2020, Journal of biomolecular structure & dynamics.

An in-silico study on selected organosulfur compounds as potential drugs for SARS-CoV-2 infection via binding multiple drug targets

P. Kar, Mintu Porel, R. Roy, 2020, Chemical Physics Letters.

Conformational preferences of triantennary and tetraantennary hybrid N-glycans in aqueous solution: Insights from 20 μs long atomistic molecular dynamic simulations

Sayan Poddar, P. Kar, Md Fulbabu Sk, 2020, Journal of biomolecular structure & dynamics.

Finding potent inhibitors against SARS-CoV-2 main protease through virtual screening, ADMET, and molecular dynamics simulation studies

Sayan Poddar, P. Kar, Md Fulbabu Sk, 2020, Journal of biomolecular structure & dynamics.

Effect of Sulfation on the Conformational Dynamics of Dermatan Sulfate Glycosaminoglycan: A Gaussian Accelerated Molecular Dynamics Study.

P. Kar, N. A. Jonniya, R. Roy, 2022, The journal of physical chemistry. B.

Comparative Structural Dynamics of Isoforms of Helicobacter pylori Adhesin BabA Bound to Lewis b Hexasaccharide via Multiple Replica Molecular Dynamics Simulations

P. Kar, Md Fulbabu Sk, N. A. Jonniya, 2022, Frontiers in Molecular Biosciences.

Exploring the potency of currently used drugs against HIV-1 protease of subtype D variant by using multiscale simulations

P. Kar, Md Fulbabu Sk, R. Roy, 2020, Journal of biomolecular structure & dynamics.

Investigating specificity of the anti-hypertensive inhibitor WNK463 against With-No-Lysine kinase family isoforms via multiscale simulations

P. Kar, N. A. Jonniya, 2019, Journal of biomolecular structure & dynamics.

Plant-derived natural polyphenols as potential antiviral drugs against SARS-CoV-2 via RNA‐dependent RNA polymerase (RdRp) inhibition: an in-silico analysis

A. Sonawane, P. Kar, Md Fulbabu Sk, 2020, Journal of biomolecular structure & dynamics.

Ethyl Pyruvate as a Potential Defense Intervention against Cytokine Storm in COVID-19?

Omprakash Tanwar, P. Pandey, P. Kar, 2021, ACS omega.

Unraveling the Molecular Mechanism of Recognition of Selected Next-Generation Antirheumatoid Arthritis Inhibitors by Janus Kinase 1

P. Kar, Md Fulbabu Sk, N. A. Jonniya, 2022, ACS omega.

Hybrid All-Atom/Coarse-Grained Simulations of Proteins by Direct Coupling of CHARMM and PRIMO Force Fields.

M. Feig, P. Kar, 2017, Journal of chemical theory and computation.

A plausible contributor to multiple sclerosis; presentation of antigenic myelin protein epitopes by major histocompatibility complexes

H. Jha, P. Kar, Md Fulbabu Sk, 2022, Comput. Biol. Medicine.

Mining of Ebola virus genome for the construction of multi-epitope vaccine to combat its infection

U. Shankar, N. Jain, Amit Kumar, 2021, Journal of biomolecular structure & dynamics.

Computational studies indicated the effectiveness of human metabolites against SARS-Cov-2 main protease

Omprakash Tanwar, P. Kar, Md Fulbabu Sk, 2022, Molecular Diversity.

Importance of polar solvation for cross-reactivity of antibody and its variants with steroids.

R. Lipowsky, V. Knecht, P. Kar, 2011, The journal of physical chemistry. B.

Functional Loop Dynamics and Characterization of the Inactive State of the NS2B-NS3 Dengue Protease due to Allosteric Inhibitor Binding

P. Kar, N. A. Jonniya, 2022, J. Chem. Inf. Model..

Role of Doxorubicin on the Loading Efficiency of ICG within Silk Fibroin Nanoparticles.

Sharad Gupta, A. Joshi, P. Kar, 2022, ACS biomaterials science & engineering.

Comparison of the conformational dynamics of an N-glycan in implicit and explicit solvents.

Sayan Poddar, P. Kar, R. Roy, 2022, Carbohydrate research.

Emerging Biomedical Applications of the Vesicular Stomatitis Virus Glycoprotein

Sharad Gupta, P. Kar, R. Roy, 2022, ACS omega.

Finding inhibitors and deciphering inhibitor-induced conformational plasticity in the Janus kinase via multiscale simulations

P. Kar, M. Sk, 2022, SAR and QSAR in environmental research.

Structure-based design and synthesis of a novel long-chain 4′′-alkyl ether derivative of EGCG as potent EGFR inhibitor: in vitro and in silico studies

P. Kar, Priya Ghosh, R. Roy, 2022, RSC advances.

Decoding the Host-Parasite Protein Interactions Involved in Cerebral Malaria Through Glares of Molecular Dynamics Simulations.

H. Jha, P. Kar, Omkar Indari, 2022, The journal of physical chemistry. B.

Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations

Sayan Poddar, P. Kar, Md Fulbabu Sk, 2020, Journal of biomolecular structure & dynamics.

Investigating Phosphorylation-Induced Conformational Changes in WNK1 Kinase by Molecular Dynamics Simulations

P. Kar, Md Fulbabu Sk, N. A. Jonniya, 2019, ACS omega.

Molecular Mechanism of Inhibiting WNK Binding to OSR1 by Targeting the Allosteric Pocket of the OSR1-CCT Domain with Potential Antihypertensive Inhibitors: An In Silico Study.

P. Kar, Jinwei Zhang, N. A. Jonniya, 2021, The journal of physical chemistry. B.

Identification of novel efflux pump inhibitors for Neisseria gonorrhoeae via multiple ligand-based pharmacophores, e-pharmacophore, molecular docking, density functional theory, and molecular dynamics approaches

Ashok Kumar, A. Mishra, P. Kar, 2022, Comput. Biol. Chem..

Unraveling the Molecular Mechanism of Recognition of Human Interferon-Stimulated Gene Product 15 by Coronavirus Papain-Like Proteases: A Multiscale Simulation Study

Sayan Poddar, P. Kar, Md Fulbabu Sk, 2021, J. Chem. Inf. Model..

The Evolutionarily Conserved C-terminal Domains in the Mammalian Retinoblastoma Tumor Suppressor Family Serve as Dual Regulators of Protein Stability and Transcriptional Potency*

D. Arnosti, M. Feig, Satyaki Sengupta, 2015, The Journal of Biological Chemistry.

A comparative study of structural and conformational properties of WNK kinase isoforms bound to an inhibitor: insights from molecular dynamic simulations

P. Kar, Md Fulbabu Sk, N. A. Jonniya, 2020, Journal of biomolecular structure & dynamics.

An in-silico study on selected organosulfur compounds as potential drugs for SARS-CoV-2 infection via binding multiple drug targets

P. Kar, Mintu Porel, R. Roy, 2020, Chemical Physics Letters.

Finding potential inhibitors against RNA-dependent RNA polymerase (RdRp) of bovine ephemeral fever virus (BEFV): an in-silico study

D. Nayak, P. Kar, Md Fulbabu Sk, 2021, Journal of biomolecular structure & dynamics.

Anti-Hemagglutinin Antibody Derived Lead Peptides for Inhibitors of Influenza Virus Binding

F. Bier, V. Knecht, A. Herrmann, 2016, PloS one.

Phosphorylation-Induced Conformational Dynamics and Inhibition of Janus Kinase 1 by Suppressors of Cytokine Signaling 1.

P. Kar, Md Fulbabu Sk, N. A. Jonniya, 2022, The journal of physical chemistry. B.

Identification of Potential Inhibitors against Epstein-Barr Virus Nuclear Antigen 1 (EBNA1): An Insight from Docking and Molecular Dynamic Simulations.

H. Jha, P. Kar, Md Fulbabu Sk, 2021, ACS chemical neuroscience.

Origin of decrease in potency of darunavir and two related antiviral inhibitors against HIV-2 compared to HIV-1 protease.

Parimal Kar, Volker Knecht, V. Knecht, 2012, The journal of physical chemistry. B.

Mutation-induced loop opening and energetics for binding of tamiflu to influenza N8 neuraminidase.

Parimal Kar, Volker Knecht, V. Knecht, 2012, The journal of physical chemistry. B.

The FGF/FGFR signalling mediated anti-cancer drug resistance and therapeutic intervention

Subhasmita Mahapatra, P. Kar, S. Koirala, 2023, Journal of biomolecular structure & dynamics.

Transferring the PRIMO Coarse-Grained Force Field to the Membrane Environment: Simulations of Membrane Proteins and Helix–Helix Association

Michael Feig, Afra Panahi, Parimal Kar, 2014, Journal of chemical theory and computation.

Algorithmic Refinements to an Enhanced Poisson-Boltzmann Approach Used in BioMolecular Simulation

Parimal Kar, Max Seel, P. Kar, 2007 .

Plant-derived active compounds as a potential nucleocapsid protein inhibitor of SARS-CoV-2: an in-silico study

H. Jha, P. Kar, R. Roy, 2022, Journal of biomolecular structure & dynamics.

Energetic basis for drug resistance of HIV-1 protease mutants against amprenavir

Parimal Kar, Volker Knecht, V. Knecht, 2012, Journal of Computer-Aided Molecular Design.

Systematic study of the boundary composition in Poisson Boltzmann calculations

Yanjie Wei, Ulrich H. E. Hansmann, Siegfried Höfinger, 2007, J. Comput. Chem..

Discovery of potential competitive inhibitors against With-No-Lysine kinase 1 for treating hypertension by virtual screening, inverse pharmacophore-based lead optimization, and molecular dynamics simulations

P. Kar, N. A. Jonniya, R. Roy, 2022, SAR and QSAR in environmental research.

Elucidating specificity of an allosteric inhibitor WNK476 among With‐No‐Lysine kinase isoforms using molecular dynamic simulations

P. Kar, Md Fulbabu Sk, Nisha Amarnath Jonniya, 2021, Chemical biology & drug design.

Characterizing an allosteric inhibitor-induced inactive state in with-no-lysine kinase 1 using Gaussian accelerated molecular dynamics simulations.

P. Kar, Md Fulbabu Sk, N. A. Jonniya, 2021, Physical chemistry chemical physics : PCCP.

Investigating potency of TMC-126 against wild-type and mutant variants of HIV-1 protease: a molecular dynamics and free energy study

M. Sk, P. Kar, R. Roy, 2021, SAR and QSAR in environmental research.

Identification of Food Compounds as inhibitors of SARS-CoV-2 main protease using molecular docking and molecular dynamics simulations

M. Zaki, V. Rastija, P. Kar, 2021, Chemometrics and Intelligent Laboratory Systems.

Energetics of mutation-induced changes in potency of lersivirine against HIV-1 reverse transcriptase.

V. Knecht, P. Kar, 2012, The journal of physical chemistry. B.

Molecular dynamics simulations reveal phosphorylation-induced conformational dynamics of the fibroblast growth factor receptor 1 kinase

Subhasmita Mahapatra, P. Kar, S. Koirala, 2023, Journal of biomolecular structure & dynamics.

Structural analysis of human ATE1 isoforms and their interactions with Arg-tRNAArg.

Sayan Poddar, V. S. Mattaparthi, P. Kar, 2023, Journal of biomolecular structure & dynamics.

Withania somnifera extract reduces gastric cancerous properties through inhibition of gankyrin in cellular milieu produced by Helicobacter pylori and Epstein Barr virus.

H. Jha, S Kumar, P. Kar, 2023, Journal of biomolecular structure & dynamics.

Computer-aided Affinity Enhancement of a Cross-reactive Antibody against Dengue Virus Envelope Domain III

Sayan Poddar, Subhasmita Mahapatra, P. Kar, 2023, Cell Biochemistry and Biophysics.

The conformational dynamics of Hepatitis C Virus E2 glycoprotein with the increasing number of N-glycosylation unraveled by molecular dynamics simulations.

Sayan Poddar, P. Kar, R. Roy, 2024, Journal of biomolecular structure & dynamics.

Deciphering the molecular choreography of Janus kinase 2 inhibition via Gaussian accelerated molecular dynamics simulations: a dynamic odyssey

Sayan Poddar, P. Kar, Md Fulbabu Sk, 2024, J. Comput. Aided Mol. Des..

Protein S-palmitoylation is markedly inhibited by 4″-alkyl ether lipophilic derivatives of EGCG, the major green tea polyphenol: In vitro and in silico studies.

Sayan Poddar, P. Kar, Sushabhan Sadhukhan, 2023, Biochimica et biophysica acta. Biomembranes.

Activation-induced cytidine deaminase an antibody diversification enzyme interacts with chromatin modifier UBN1 in B-cells

Prashant Kodgire, P. Kar, Ankit Jaiswal, 2023, Scientific reports.

Computational insights into VacA toxin inhibition: harnessing FDA-approved antibiotics against Helicobacter pylori.

H. Jha, P. Kar, R. Roy, 2023, Journal of biomolecular structure & dynamics.

Molecular level investigation for identifying potential inhibitors against thymidylate kinase of monkeypox through in silico approaches.

Sayan Poddar, Subhasmita Mahapatra, P. Kar, 2023, Journal of biomolecular structure & dynamics.

Elucidating the conformational dynamics of histo-blood group antigens and their interactions with the rotavirus spike protein through computational lens.

Sayan Poddar, P. Kar, R. Roy, 2023, Journal of biomolecular structure & dynamics.

Exploring molecular interactions of potential inhibitors against the spleen tyrosine kinase implicated in autoimmune disorders via virtual screening and molecular dynamics simulations

P. Kar, M. Sk, S. Samanta, 2023, SAR and QSAR in environmental research.

Microsecond dynamics of H10N7 influenza neuraminidase reveals the plasticity of loop regions and drug resistance due to the R292K mutation

Sayan Poddar, P. Kar, Md Fulbabu Sk, 2023, J. Comput. Chem..

Development of chalcone-like derivatives and their biological and mechanistic investigations as novel influenza nuclear export inhibitors.

P. Zhan, Xinyong Liu, P. Kar, 2023, European journal of medicinal chemistry.

Prediction of Rab5B inhibitors through integrative in silico techniques

H. Jha, P. Kar, S. Koirala, 2023, Molecular diversity.

4″-Alkyl EGCG Derivatives Induce Cytoprotective Autophagy Response by Inhibiting EGFR in Glioblastoma Cells

P. Kar, R. Roy, Ananyaashree Behera, 2024, ACS omega.

Conformational preferences of triantennary and tetraantennary hybrid N-glycans in aqueous solution: Insights from 20 μs long atomistic molecular dynamic simulations

Sayan Poddar, P. Kar, Md Fulbabu Sk, 2022, Journal of biomolecular structure & dynamics.

Microcanonical replica exchange molecular dynamics simulation of proteins.

Ulrich H E Hansmann, Walter Nadler, Parimal Kar, 2009, Physical review. E, Statistical, nonlinear, and soft matter physics.

Computational Biophysical Characterization of the Effect of Gatekeeper Mutations on the Binding of Ponatinib to the FGFR Kinase.

Subhasmita Mahapatra, P. Kar, 2024, Archives of biochemistry and biophysics.

Dispersion terms and analysis of size- and charge dependence in an enhanced Poisson-Boltzmann approach.

Ulrich H E Hansmann, Siegfried Höfinger, Parimal Kar, 2007, The journal of physical chemistry. B.