Md Fulbabu Sk, Rajarshi Roy, Nisha Amarnath Jonniya, Sayan Poddar, Parimal Kar. J Biomol Struct Dyn 2021
Times Cited: 40
Times Cited: 40
Times Cited
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Exploring the energetic basis of binding of currently used drugs against HIV-1 subtype CRF01_AE protease via molecular dynamics simulations.
Md Fulbabu Sk, Nisha Amarnath Jonniya, Parimal Kar. J Biomol Struct Dyn 2021
Md Fulbabu Sk, Nisha Amarnath Jonniya, Parimal Kar. J Biomol Struct Dyn 2021
95
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data.
Daniel R Roe, Thomas E Cheatham. J Chem Theory Comput 2013
Daniel R Roe, Thomas E Cheatham. J Chem Theory Comput 2013
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ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB.
James A Maier, Carmenza Martinez, Koushik Kasavajhala, Lauren Wickstrom, Kevin E Hauser, Carlos Simmerling. J Chem Theory Comput 2015
James A Maier, Carmenza Martinez, Koushik Kasavajhala, Lauren Wickstrom, Kevin E Hauser, Carlos Simmerling. J Chem Theory Comput 2015
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Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models.
P A Kollman, I Massova, C Reyes, B Kuhn, S Huo, L Chong, M Lee, T Lee, Y Duan, W Wang,[...]. Acc Chem Res 2000
P A Kollman, I Massova, C Reyes, B Kuhn, S Huo, L Chong, M Lee, T Lee, Y Duan, W Wang,[...]. Acc Chem Res 2000
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Development and testing of a general amber force field.
Junmei Wang, Romain M Wolf, James W Caldwell, Peter A Kollman, David A Case. J Comput Chem 2004
Junmei Wang, Romain M Wolf, James W Caldwell, Peter A Kollman, David A Case. J Comput Chem 2004
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UCSF Chimera--a visualization system for exploratory research and analysis.
Eric F Pettersen, Thomas D Goddard, Conrad C Huang, Gregory S Couch, Daniel M Greenblatt, Elaine C Meng, Thomas E Ferrin. J Comput Chem 2004
Eric F Pettersen, Thomas D Goddard, Conrad C Huang, Gregory S Couch, Daniel M Greenblatt, Elaine C Meng, Thomas E Ferrin. J Comput Chem 2004
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AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading.
Oleg Trott, Arthur J Olson. J Comput Chem 2010
Oleg Trott, Arthur J Olson. J Comput Chem 2010
37
Investigating Phosphorylation-Induced Conformational Changes in WNK1 Kinase by Molecular Dynamics Simulations.
Nisha Amarnath Jonniya, Md Fulbabu Sk, Parimal Kar. ACS Omega 2019
Nisha Amarnath Jonniya, Md Fulbabu Sk, Parimal Kar. ACS Omega 2019
55
Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors.
Linlin Zhang, Daizong Lin, Xinyuanyuan Sun, Ute Curth, Christian Drosten, Lucie Sauerhering, Stephan Becker, Katharina Rox, Rolf Hilgenfeld. Science 2020
Linlin Zhang, Daizong Lin, Xinyuanyuan Sun, Ute Curth, Christian Drosten, Lucie Sauerhering, Stephan Becker, Katharina Rox, Rolf Hilgenfeld. Science 2020
35
Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors.
Zhenming Jin, Xiaoyu Du, Yechun Xu, Yongqiang Deng, Meiqin Liu, Yao Zhao, Bing Zhang, Xiaofeng Li, Leike Zhang, Chao Peng,[...]. Nature 2020
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32
Marine natural compounds as potents inhibitors against the main protease of SARS-CoV-2-a molecular dynamic study.
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30
Investigating Conformational Dynamics of Lewis Y Oligosaccharides and Elucidating Blood Group Dependency of Cholera Using Molecular Dynamics.
Rajarshi Roy, Biplab Ghosh, Parimal Kar. ACS Omega 2020
Rajarshi Roy, Biplab Ghosh, Parimal Kar. ACS Omega 2020
63
Investigating specificity of the anti-hypertensive inhibitor WNK463 against With-No-Lysine kinase family isoforms via multiscale simulations.
Nisha A Jonniya, Parimal Kar. J Biomol Struct Dyn 2020
Nisha A Jonniya, Parimal Kar. J Biomol Struct Dyn 2020
60
Computational studies of drug repurposing and synergism of lopinavir, oseltamivir and ritonavir binding with SARS-CoV-2 protease against COVID-19.
Nisha Muralidharan, R Sakthivel, D Velmurugan, M Michael Gromiha. J Biomol Struct Dyn 2021
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27
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27
Importance of polar solvation for cross-reactivity of antibody and its variants with steroids.
Parimal Kar, Reinhard Lipowsky, Volker Knecht. J Phys Chem B 2011
Parimal Kar, Reinhard Lipowsky, Volker Knecht. J Phys Chem B 2011
35
Exploring the potency of currently used drugs against HIV-1 protease of subtype D variant by using multiscale simulations.
Md Fulbabu Sk, Rajarshi Roy, Parimal Kar. J Biomol Struct Dyn 2021
Md Fulbabu Sk, Rajarshi Roy, Parimal Kar. J Biomol Struct Dyn 2021
50
Targeting SARS-CoV-2: a systematic drug repurposing approach to identify promising inhibitors against 3C-like proteinase and 2'-O-ribose methyltransferase.
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25
Potential anti-viral activity of approved repurposed drug against main protease of SARS-CoV-2: an in silico based approach.
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SARS-CoV-2 RNA dependent RNA polymerase (RdRp) targeting: an in silico perspective.
Abdo A Elfiky. J Biomol Struct Dyn 2021
Abdo A Elfiky. J Biomol Struct Dyn 2021
25
Energetics of mutation-induced changes in potency of lersivirine against HIV-1 reverse transcriptase.
Parimal Kar, Volker Knecht. J Phys Chem B 2012
Parimal Kar, Volker Knecht. J Phys Chem B 2012
43
Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation.
Araz Jakalian, David B Jack, Christopher I Bayly. J Comput Chem 2002
Araz Jakalian, David B Jack, Christopher I Bayly. J Comput Chem 2002
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Andrographolide as a potential inhibitor of SARS-CoV-2 main protease: an in silico approach.
Sukanth Kumar Enmozhi, Kavitha Raja, Irudhayasamy Sebastine, Jerrine Joseph. J Biomol Struct Dyn 2021
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22
A molecular modeling approach to identify effective antiviral phytochemicals against the main protease of SARS-CoV-2.
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Identification of bioactive molecules from tea plant as SARS-CoV-2 main protease inhibitors.
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Identification of chymotrypsin-like protease inhibitors of SARS-CoV-2 via integrated computational approach.
Salman Ali Khan, Komal Zia, Sajda Ashraf, Reaz Uddin, Zaheer Ul-Haq. J Biomol Struct Dyn 2021
Salman Ali Khan, Komal Zia, Sajda Ashraf, Reaz Uddin, Zaheer Ul-Haq. J Biomol Struct Dyn 2021
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Novel 2019 coronavirus structure, mechanism of action, antiviral drug promises and rule out against its treatment.
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Subramanian Boopathi, Adolfo B Poma, Ponmalai Kolandaivel. J Biomol Struct Dyn 2021
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An investigation into the identification of potential inhibitors of SARS-CoV-2 main protease using molecular docking study.
Sourav Das, Sharat Sarmah, Sona Lyndem, Atanu Singha Roy. J Biomol Struct Dyn 2021
Sourav Das, Sharat Sarmah, Sona Lyndem, Atanu Singha Roy. J Biomol Struct Dyn 2021
22
Automatic atom type and bond type perception in molecular mechanical calculations.
Junmei Wang, Wei Wang, Peter A Kollman, David A Case. J Mol Graph Model 2006
Junmei Wang, Wei Wang, Peter A Kollman, David A Case. J Mol Graph Model 2006
22
Energetic basis for drug resistance of HIV-1 protease mutants against amprenavir.
Parimal Kar, Volker Knecht. J Comput Aided Mol Des 2012
Parimal Kar, Volker Knecht. J Comput Aided Mol Des 2012
22
Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes.
Holger Gohlke, Christina Kiel, David A Case. J Mol Biol 2003
Holger Gohlke, Christina Kiel, David A Case. J Mol Biol 2003
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Origin of decrease in potency of darunavir and two related antiviral inhibitors against HIV-2 compared to HIV-1 protease.
Parimal Kar, Volker Knecht. J Phys Chem B 2012
Parimal Kar, Volker Knecht. J Phys Chem B 2012
22
Plant-derived natural polyphenols as potential antiviral drugs against SARS-CoV-2 via RNA-dependent RNA polymerase (RdRp) inhibition: an in-silico analysis.
Satyam Singh, Md Fulbabu Sk, Avinash Sonawane, Parimal Kar, Sushabhan Sadhukhan. J Biomol Struct Dyn 2021
Satyam Singh, Md Fulbabu Sk, Avinash Sonawane, Parimal Kar, Sushabhan Sadhukhan. J Biomol Struct Dyn 2021
22
A comparative study of structural and conformational properties of WNK kinase isoforms bound to an inhibitor: insights from molecular dynamic simulations.
Nisha Amarnath Jonniya, Md Fulbabu Sk, Parimal Kar. J Biomol Struct Dyn 2022
Nisha Amarnath Jonniya, Md Fulbabu Sk, Parimal Kar. J Biomol Struct Dyn 2022
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Understanding the binding affinity of noscapines with protease of SARS-CoV-2 for COVID-19 using MD simulations at different temperatures.
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Durgesh Kumar, Kamlesh Kumari, Abhilash Jayaraj, Vinod Kumar, Ramappa Venkatesh Kumar, Sujata K Dass, Ramesh Chandra, Prashant Singh. J Biomol Struct Dyn 2021
20
Natural products may interfere with SARS-CoV-2 attachment to the host cell.
Abdo A Elfiky. J Biomol Struct Dyn 2021
Abdo A Elfiky. J Biomol Struct Dyn 2021
20
Development of remdesivir repositioning as a nucleotide analog against COVID-19 RNA dependent RNA polymerase.
Mohammad Mahdi Nejadi Babadaei, Anwarul Hasan, Yasaman Vahdani, Samir Haj Bloukh, Majid Sharifi, Ehsan Kachooei, Setareh Haghighat, Mojtaba Falahati. J Biomol Struct Dyn 2021
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Discovery of potential multi-target-directed ligands by targeting host-specific SARS-CoV-2 structurally conserved main protease.
Rakesh S Joshi, Shounak S Jagdale, Sneha B Bansode, S Shiva Shankar, Meenakshi B Tellis, Vaibhav Kumar Pandya, Anita Chugh, Ashok P Giri, Mahesh J Kulkarni. J Biomol Struct Dyn 2021
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Identification of potential molecules against COVID-19 main protease through structure-guided virtual screening approach.
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An in-silico evaluation of different Saikosaponins for their potency against SARS-CoV-2 using NSP15 and fusion spike glycoprotein as targets.
Saurabh K Sinha, Anshul Shakya, Satyendra K Prasad, Shashikant Singh, Nilambari S Gurav, Rupali S Prasad, Shailendra S Gurav. J Biomol Struct Dyn 2021
Saurabh K Sinha, Anshul Shakya, Satyendra K Prasad, Shashikant Singh, Nilambari S Gurav, Rupali S Prasad, Shailendra S Gurav. J Biomol Struct Dyn 2021
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Stilbene-based natural compounds as promising drug candidates against COVID-19.
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Hussain Mustatab Wahedi, Sajjad Ahmad, Sumra Wajid Abbasi. J Biomol Struct Dyn 2021
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Moroccan Medicinal plants as inhibitors against SARS-CoV-2 main protease: Computational investigations.
I Aanouz, A Belhassan, K El-Khatabi, T Lakhlifi, M El-Ldrissi, M Bouachrine. J Biomol Struct Dyn 2021
I Aanouz, A Belhassan, K El-Khatabi, T Lakhlifi, M El-Ldrissi, M Bouachrine. J Biomol Struct Dyn 2021
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Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods.
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Canrong Wu, Yang Liu, Yueying Yang, Peng Zhang, Wu Zhong, Yali Wang, Qiqi Wang, Yang Xu, Mingxue Li, Xingzhou Li,[...]. Acta Pharm Sin B 2020
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Langevin dynamics of peptides: the frictional dependence of isomerization rates of N-acetylalanyl-N'-methylamide.
R J Loncharich, B R Brooks, R W Pastor. Biopolymers 1992
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A modified TIP3P water potential for simulation with Ewald summation.
Daniel J Price, Charles L Brooks. J Chem Phys 2004
Daniel J Price, Charles L Brooks. J Chem Phys 2004
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Computational Investigation of Structural Dynamics of SARS-CoV-2 Methyltransferase-Stimulatory Factor Heterodimer nsp16/nsp10 Bound to the Cofactor SAM.
Md Fulbabu Sk, Nisha Amarnath Jonniya, Rajarshi Roy, Sayan Poddar, Parimal Kar. Front Mol Biosci 2020
Md Fulbabu Sk, Nisha Amarnath Jonniya, Rajarshi Roy, Sayan Poddar, Parimal Kar. Front Mol Biosci 2020
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Using integrated computational approaches to identify safe and rapid treatment for SARS-CoV-2.
Khattab Al-Khafaji, Dunya Al-Duhaidahawi, Tugba Taskin Tok. J Biomol Struct Dyn 2021
Khattab Al-Khafaji, Dunya Al-Duhaidahawi, Tugba Taskin Tok. J Biomol Struct Dyn 2021
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Identification of new anti-nCoV drug chemical compounds from Indian spices exploiting SARS-CoV-2 main protease as target.
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Debanjan Kundu, Chandrabose Selvaraj, Sanjeev Kumar Singh, Vikash Kumar Dubey. J Biomol Struct Dyn 2021
17
In-silico homology assisted identification of inhibitor of RNA binding against 2019-nCoV N-protein (N terminal domain).
Phulen Sarma, Nishant Shekhar, Manisha Prajapat, Pramod Avti, Hardeep Kaur, Subodh Kumar, Sanjay Singh, Harish Kumar, Ajay Prakash, Deba Prasad Dhibar,[...]. J Biomol Struct Dyn 2021
Phulen Sarma, Nishant Shekhar, Manisha Prajapat, Pramod Avti, Hardeep Kaur, Subodh Kumar, Sanjay Singh, Harish Kumar, Ajay Prakash, Deba Prasad Dhibar,[...]. J Biomol Struct Dyn 2021
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Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.