Md Fulbabu Sk, Nisha Amarnath Jonniya, Parimal Kar. J Biomol Struct Dyn 2021
Times Cited: 22
Times Cited: 22
Times Cited
Times Co-cited
Similarity
Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations.
Md Fulbabu Sk, Rajarshi Roy, Nisha Amarnath Jonniya, Sayan Poddar, Parimal Kar. J Biomol Struct Dyn 2021
Md Fulbabu Sk, Rajarshi Roy, Nisha Amarnath Jonniya, Sayan Poddar, Parimal Kar. J Biomol Struct Dyn 2021
95
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
59
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
59
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
59
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
54
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
54
Targeting SARS-CoV-2: a systematic drug repurposing approach to identify promising inhibitors against 3C-like proteinase and 2'-O-ribose methyltransferase.
Rameez Jabeer Khan, Rajat Kumar Jha, Gizachew Muluneh Amera, Monika Jain, Ekampreet Singh, Amita Pathak, Rashmi Prabha Singh, Jayaraman Muthukumaran, Amit Kumar Singh. J Biomol Struct Dyn 2021
Rameez Jabeer Khan, Rajat Kumar Jha, Gizachew Muluneh Amera, Monika Jain, Ekampreet Singh, Amita Pathak, Rashmi Prabha Singh, Jayaraman Muthukumaran, Amit Kumar Singh. J Biomol Struct Dyn 2021
45
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
45
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
45
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
50
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
45
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
40
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
40
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
40
A molecular modeling approach to identify effective antiviral phytochemicals against the main protease of SARS-CoV-2.
Rajib Islam, Md Rimon Parves, Archi Sundar Paul, Nizam Uddin, Md Sajjadur Rahman, Abdulla Al Mamun, Md Nayeem Hossain, Md Ackas Ali, Mohammad A Halim. J Biomol Struct Dyn 2021
Rajib Islam, Md Rimon Parves, Archi Sundar Paul, Nizam Uddin, Md Sajjadur Rahman, Abdulla Al Mamun, Md Nayeem Hossain, Md Ackas Ali, Mohammad A Halim. J Biomol Struct Dyn 2021
40
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
42
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
Nisha Muralidharan, R Sakthivel, D Velmurugan, M Michael Gromiha. J Biomol Struct Dyn 2021
40
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
36
Novel 2019 coronavirus structure, mechanism of action, antiviral drug promises and rule out against its treatment.
Subramanian Boopathi, Adolfo B Poma, Ponmalai Kolandaivel. J Biomol Struct Dyn 2021
Subramanian Boopathi, Adolfo B Poma, Ponmalai Kolandaivel. J Biomol Struct Dyn 2021
36
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
36
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
R J Loncharich, B R Brooks, R W Pastor. Biopolymers 1992
36
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
36
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
36
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
36
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
36
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
36
Drug repurposing for coronavirus (COVID-19): in silico screening of known drugs against coronavirus 3CL hydrolase and protease enzymes.
Ammar D Elmezayen, Anas Al-Obaidi, Alp Tegin Şahin, Kemal Yelekçi. J Biomol Struct Dyn 2021
Ammar D Elmezayen, Anas Al-Obaidi, Alp Tegin Şahin, Kemal Yelekçi. J Biomol Struct Dyn 2021
36
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
36
Marine natural compounds as potents inhibitors against the main protease of SARS-CoV-2-a molecular dynamic study.
Muhammad Tahir Khan, Arif Ali, Qiankun Wang, Muhammad Irfan, Abbas Khan, Muhammad Tariq Zeb, Yu-Juan Zhang, Sathishkumar Chinnasamy, Dong-Qing Wei. J Biomol Struct Dyn 2021
Muhammad Tahir Khan, Arif Ali, Qiankun Wang, Muhammad Irfan, Abbas Khan, Muhammad Tariq Zeb, Yu-Juan Zhang, Sathishkumar Chinnasamy, Dong-Qing Wei. J Biomol Struct Dyn 2021
36
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
66
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
44
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
31
The energy landscapes and motions of proteins.
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LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions.
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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
31
Collective motions in proteins: a covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations.
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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
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
31
Importance of polar solvation and configurational entropy for design of antiretroviral drugs targeting HIV-1 protease.
Parimal Kar, Reinhard Lipowsky, Volker Knecht. J Phys Chem B 2013
Parimal Kar, Reinhard Lipowsky, Volker Knecht. J Phys Chem B 2013
31
Stilbene-based natural compounds as promising drug candidates against COVID-19.
Hussain Mustatab Wahedi, Sajjad Ahmad, Sumra Wajid Abbasi. J Biomol Struct Dyn 2021
Hussain Mustatab Wahedi, Sajjad Ahmad, Sumra Wajid Abbasi. J Biomol Struct Dyn 2021
31
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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Novel guanosine derivatives against MERS CoV polymerase: An in silico perspective.
Abdo A Elfiky, Eman B Azzam. J Biomol Struct Dyn 2021
Abdo A Elfiky, Eman B Azzam. J Biomol Struct Dyn 2021
31
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
Sukanth Kumar Enmozhi, Kavitha Raja, Irudhayasamy Sebastine, Jerrine Joseph. J Biomol Struct Dyn 2021
31
Repurposing of chloroquine and some clinically approved antiviral drugs as effective therapeutics to prevent cellular entry and replication of coronavirus.
Akinwunmi O Adeoye, Babatunde Joseph Oso, Ige Francis Olaoye, Habibu Tijjani, Ahmed I Adebayo. J Biomol Struct Dyn 2021
Akinwunmi O Adeoye, Babatunde Joseph Oso, Ige Francis Olaoye, Habibu Tijjani, Ahmed I Adebayo. J Biomol Struct Dyn 2021
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Potential anti-viral activity of approved repurposed drug against main protease of SARS-CoV-2: an in silico based approach.
Saurov Mahanta, Purvita Chowdhury, Neelutpal Gogoi, Nabajyoti Goswami, Debajit Borah, Rupesh Kumar, Dipak Chetia, Probodh Borah, Alak K Buragohain, Bhaskarjyoti Gogoi. J Biomol Struct Dyn 2021
Saurov Mahanta, Purvita Chowdhury, Neelutpal Gogoi, Nabajyoti Goswami, Debajit Borah, Rupesh Kumar, Dipak Chetia, Probodh Borah, Alak K Buragohain, Bhaskarjyoti Gogoi. J Biomol Struct Dyn 2021
31
Identification of bioactive molecules from tea plant as SARS-CoV-2 main protease inhibitors.
Vijay Kumar Bhardwaj, Rahul Singh, Jatin Sharma, Vidya Rajendran, Rituraj Purohit, Sanjay Kumar. J Biomol Struct Dyn 2021
Vijay Kumar Bhardwaj, Rahul Singh, Jatin Sharma, Vidya Rajendran, Rituraj Purohit, Sanjay Kumar. J Biomol Struct Dyn 2021
31
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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Identification of new anti-nCoV drug chemical compounds from Indian spices exploiting SARS-CoV-2 main protease as target.
Debanjan Kundu, Chandrabose Selvaraj, Sanjeev Kumar Singh, Vikash Kumar Dubey. J Biomol Struct Dyn 2021
Debanjan Kundu, Chandrabose Selvaraj, Sanjeev Kumar Singh, Vikash Kumar Dubey. J Biomol Struct Dyn 2021
27
PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions.
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Peptide-like and small-molecule inhibitors against Covid-19.
Suyash Pant, Meenakshi Singh, V Ravichandiran, U S N Murty, Hemant Kumar Srivastava. J Biomol Struct Dyn 2021
Suyash Pant, Meenakshi Singh, V Ravichandiran, U S N Murty, Hemant Kumar Srivastava. J Biomol Struct Dyn 2021
27
In silico study the inhibition of angiotensin converting enzyme 2 receptor of COVID-19 by Ammoides verticillata components harvested from Western Algeria.
Imane Abdelli, Faiçal Hassani, Sohayb Bekkel Brikci, Said Ghalem. J Biomol Struct Dyn 2021
Imane Abdelli, Faiçal Hassani, Sohayb Bekkel Brikci, Said Ghalem. 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.