☰

Jagannath Mondal, Ph.D - Publications

Affiliations: 
TIFR Centre for Interdisciplinary Sciences  
Area:
Computer simulations
Tree Info Similar researchers PubMed Report error

50 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Dandekar BR, Majumdar BB, Mondal J. Nonmonotonic Modulation of the Protein-Ligand Recognition Event by Inert Crowders. The Journal of Physical Chemistry. B. 127: 7449-7461. PMID 37590118 DOI: 10.1021/acs.jpcb.3c03946  0.78
2023 Ahalawat N, Sahil M, Mondal J. Resolving Protein Conformational Plasticity and Substrate Binding via Machine Learning. Journal of Chemical Theory and Computation. PMID 37068044 DOI: 10.1021/acs.jctc.2c00932  0.316
2022 Majumdar BB, Mondal J. Impact of Inert Crowders on Host-Guest Recognition Process. The Journal of Physical Chemistry. B. PMID 35654414 DOI: 10.1021/acs.jpcb.2c01539  0.765
2022 Bandyopadhyay S, Majumdar BB, Mondal J. Solvent's Role in Cavity-Ligand Recognition Would Depend on the Mode of Ligand Diffusion. The Journal of Physical Chemistry. B. PMID 35436126 DOI: 10.1021/acs.jpcb.1c09645  0.764
2021 Koneru JK, Sinha S, Mondal J. Molecular Dynamics Simulations Elucidate Oligosaccharide Recognition Pathways by Galectin-3 at Atomic Resolution. The Journal of Biological Chemistry. 101271. PMID 34619151 DOI: 10.1016/j.jbc.2021.101271  0.315
2020 Mukherjee M, Mondal J. Bottom-Up View of the Mechanism of Action of Protein-Stabilizing Osmolytes. The Journal of Physical Chemistry. B. PMID 33198465 DOI: 10.1021/acs.jpcb.0c06658  0.782
2020 Mukherjee M, Mondal J. Unifying the Contrasting Mechanisms of Protein-Stabilising Osmolytes. The Journal of Physical Chemistry. B. PMID 32633959 DOI: 10.1021/Acs.Jpcb.0C04757  0.772
2020 Dandekar BR, Mondal J. Capturing Protein-Ligand Recognition Pathways in Coarse-Grained Simulation. The Journal of Physical Chemistry Letters. PMID 32520567 DOI: 10.1021/Acs.Jpclett.0C01683  0.443
2020 Sharma N, Ahalawat N, Sandhu P, Strauss E, Mondal J, Anand R. Role of allosteric switches and adaptor domains in long-distance cross-talk and transient tunnel formation. Science Advances. 6: eaay7919. PMID 32284973 DOI: 10.1126/Sciadv.Aay7919  0.357
2020 Prakashchand DD, Ahalawat N, Bandyopadhyay S, Sengupta S, Mondal J. Non-affine displacements encode collective conformational fluctuations in proteins. Journal of Chemical Theory and Computation. PMID 32207977 DOI: 10.1021/Acs.Jctc.9B01100  0.367
2020 Ahalawat N, Bandyopadhyay S, Mondal J. On the role of solvent in hydrophobic cavity-ligand recognition kinetics. The Journal of Chemical Physics. 152: 074104. PMID 32087659 DOI: 10.1063/1.5139584  0.417
2019 Sarkar B, Siddiqui Z, Nguyen PK, Dube N, Fu W, Park S, Jaisinghani S, Paul R, Kozuch SD, Deng D, Iglesias-Montoro P, Li M, Sabatino D, Perlin DS, Zhang W, ... Mondal J, et al. Membrane-Disrupting Nanofibrous Peptide Hydrogels. Acs Biomaterials Science & Engineering. 5: 4657-4670. PMID 33448838 DOI: 10.1021/Acsbiomaterials.9B00967  0.316
2019 Koneru JK, Zhu X, Mondal J. A Quantitative Assessment of the Conformational Heterogeneity in Amylose across Force Fields. Journal of Chemical Theory and Computation. PMID 31560849 DOI: 10.1021/Acs.Jctc.9B00630  0.337
2019 Mukherjee M, Mondal J. Osmolyte-Induced Macromolecular Aggregation Is Length-Scale Dependent. The Journal of Physical Chemistry. B. PMID 31539258 DOI: 10.1021/Acs.Jpcb.9B07746  0.764
2019 Mukherjee M, Mondal J. Osmolyte-Induced Collapse of a Charged Macromolecule. The Journal of Physical Chemistry. B. PMID 31091409 DOI: 10.1021/Acs.Jpcb.9B01383  0.746
2019 Mukherjee M, Mondal J, Karmakar S. Role of α and β relaxations in collapsing dynamics of a polymer chain in supercooled glass-forming liquid. The Journal of Chemical Physics. 150: 114503. PMID 30901993 DOI: 10.1063/1.5085077  0.76
2019 Dube D, Ahalawat N, Khandelia H, Mondal J, Sengupta S. On identifying collective displacements in apo-proteins that reveal eventual binding pathways. Plos Computational Biology. 15: e1006665. PMID 30645590 DOI: 10.1371/Journal.Pcbi.1006665  0.39
2018 Ahalawat N, Mondal J. Mapping the Substrate Recognition Pathway in Cytochrome P450. Journal of the American Chemical Society. PMID 30479124 DOI: 10.1021/Jacs.8B10840  0.359
2018 Ahalawat N, Mondal J. Assessment and optimization of collective variables for protein conformational landscape: GB1 -hairpin as a case study. The Journal of Chemical Physics. 149: 094101. PMID 30195312 DOI: 10.1063/1.5041073  0.361
2018 Mukherjee M, Mondal J. Heterogeneous Impacts of Protein-Stabilizing Osmolytes on Hydrophobic Interaction. The Journal of Physical Chemistry. B. PMID 29901998 DOI: 10.1021/Acs.Jpcb.8B04654  0.779
2018 Mondal J, Ahalawat N, Pandit S, Kay LE, Vallurupalli P. Atomic resolution mechanism of ligand binding to a solvent inaccessible cavity in T4 lysozyme. Plos Computational Biology. 14: e1006180. PMID 29775455 DOI: 10.1371/Journal.Pcbi.1006180  0.449
2018 Lyu Y, Xiang N, Mondal J, Zhu X, Narsimhan G. Characterization of Interaction Between Curcumin and Different Types of Lipid Bilayers by Molecular Dynamics Simulation. The Journal of Physical Chemistry. B. PMID 29394060 DOI: 10.1021/Acs.Jpcb.7B10566  0.304
2018 Bawari S, Narayanan TN, Mondal J. Atomistic Elucidation of Sorption Processes in Hydrogen Evolution Reaction on a van der Waals Heterostructure The Journal of Physical Chemistry C. 122: 10034-10041. DOI: 10.1021/Acs.Jpcc.8B01988  0.302
2017 Ray S, Maitra A, Biswas A, Panjikar S, Mondal J, Anand R. Functional Insights into the Mode of DNA and Ligand Binding of the TetR Family Regulator TylP from Streptomyces fradiae. The Journal of Biological Chemistry. PMID 28739805 DOI: 10.1074/Jbc.M117.788000  0.335
2017 Tiwary P, Mondal J, Berne BJ. How and when does an anticancer drug leave its binding site? Science Advances. 3: e1700014. PMID 28580424 DOI: 10.1126/Sciadv.1700014  0.688
2017 Berkovich R, Mondal J, Paster I, Berne BJ. Simulated Force Quench Dynamics Shows GB1 Protein is Not a Two State Folder. The Journal of Physical Chemistry. B. PMID 28453938 DOI: 10.1021/Acs.Jpcb.7B00610  0.559
2017 Mondal J, Berkovich R, Berne B. Is Protein Single Molecule Dynamics under Force Described by Two or More States? Biophysical Journal. 112: 31a. DOI: 10.1016/J.Bpj.2016.11.201  0.563
2016 Tah I, Mondal J. How Does a Hydrophobic Macromolecule Respond to Mixed Osmolyte Environment? The Journal of Physical Chemistry. B. PMID 27700087 DOI: 10.1021/Acs.Jpcb.6B08378  0.408
2016 Mondal J, Tiwary P, Berne BJ. How a kinase inhibitor withstands Gatekeeper residue mutations. Journal of the American Chemical Society. PMID 26954686 DOI: 10.1021/Jacs.6B01232  0.649
2016 Roy S, Skoff D, Perroni DV, Mondal J, Yethiraj A, Mahanthappa M, Zanni M, Skinner JL. Water Dynamics in Gyroid Phases of Self-Assembled Gemini Surfactants. Journal of the American Chemical Society. PMID 26875689 DOI: 10.1021/Jacs.5B12370  0.537
2015 Tiwary P, Mondal J, Morrone JA, Berne BJ. Role of water and steric constraints in the kinetics of cavity-ligand unbinding. Proceedings of the National Academy of Sciences of the United States of America. PMID 26371312 DOI: 10.1073/Pnas.1516652112  0.713
2015 Mondal J, Halverson D, Li IT, Stirnemann G, Walker GC, Berne BJ. How osmolytes influence hydrophobic polymer conformations: A unified view from experiment and theory. Proceedings of the National Academy of Sciences of the United States of America. 112: 9270-5. PMID 26170324 DOI: 10.1073/Pnas.1511780112  0.626
2015 Ghosh P, Mondal J, Ben-Jacob E, Levine H. Mechanically-driven phase separation in a growing bacterial colony. Proceedings of the National Academy of Sciences of the United States of America. 112: E2166-73. PMID 25870260 DOI: 10.1073/Pnas.1504948112  0.34
2015 Mondal J, Halverson D, Li ITS, Stirnemann G, Walker GC, Berne BJ. How osmolytes influence hydrophobic polymer conformations: A unified view from experiment and theory Proceedings of the National Academy of Sciences of the United States of America. 112: 9270-9275. DOI: 10.1073/pnas.1511780112  0.449
2015 Ghosh P, Mondal J, Ben-Jacob E, Levine H. Depletion-Mediated Pattern Formation in a Growing Bacterial Colony Biophysical Journal. 108: 601a. DOI: 10.1016/J.Bpj.2014.11.3274  0.306
2015 Mondal J, Friesner R, Berne BJ. Role of Desolvation in Thermodynamics and Kinetics of Ligand Binding to a Protein Biophysical Journal. 108: 12a. DOI: 10.1016/J.Bpj.2014.11.093  0.558
2014 Mondal J, Friesner RA, Berne BJ. Role of Desolvation in Thermodynamics and Kinetics of Ligand Binding to a Kinase. Journal of Chemical Theory and Computation. 10: 5696-5705. PMID 25516727 DOI: 10.1021/Ct500584N  0.554
2014 Choi E, Mondal J, Yethiraj A. Coarse-grained models for aqueous polyethylene glycol solutions. The Journal of Physical Chemistry. B. 118: 323-9. PMID 24350686 DOI: 10.1021/Jp408392B  0.557
2014 Mondal J, Choi E, Yethiraj A. Atomistic simulations of poly(ethylene oxide) in water and an ionic liquid at room temperature Macromolecules. 47: 438-446. DOI: 10.1021/Ma4016714  0.561
2013 Mondal J, Morrone JA, Berne BJ. How hydrophobic drying forces impact the kinetics of molecular recognition. Proceedings of the National Academy of Sciences of the United States of America. 110: 13277-82. PMID 23901110 DOI: 10.1073/Pnas.1312529110  0.597
2013 Mondal J, Stirnemann G, Berne BJ. When does trimethylamine N-oxide fold a polymer chain and urea unfold it? The Journal of Physical Chemistry. B. 117: 8723-32. PMID 23800089 DOI: 10.1021/Jp405609J  0.584
2013 Mondal J, Mahanthappa M, Yethiraj A. Self-assembly of gemini surfactants: a computer simulation study. The Journal of Physical Chemistry. B. 117: 4254-62. PMID 22967267 DOI: 10.1021/Jp304933K  0.551
2012 Mondal J, Yethiraj A. Effect of secondary structure on the self-assembly of amphiphilic molecules: a multiscale simulation study. The Journal of Chemical Physics. 136: 084902. PMID 22380061 DOI: 10.1063/1.3689298  0.554
2012 Mondal J, Zhu X, Cui Q, Yethiraj A. Sequence-dependent pKa shift induced by molecular self-assembly: insights from computer simulation. The Journal of Physical Chemistry. B. 116: 491-5. PMID 22121949 DOI: 10.1021/Jp2071953  0.56
2011 Mondal J, Bratton BP, Li Y, Yethiraj A, Weisshaar JC. Entropy-based mechanism of ribosome-nucleoid segregation in E. coli cells. Biophysical Journal. 100: 2605-13. PMID 21641305 DOI: 10.1016/J.Bpj.2011.04.030  0.522
2011 Mondal J, Yethiraj A. Driving Force for the Association of Amphiphilic Molecules The Journal of Physical Chemistry Letters. 2: 2391-2395. DOI: 10.1021/Jz201046X  0.556
2010 Mondal J, Zhu X, Cui Q, Yethiraj A. Sequence-dependent interaction of β-peptides with membranes. The Journal of Physical Chemistry. B. 114: 13585-92. PMID 20882985 DOI: 10.1021/Jp1070242  0.547
2010 Mondal J, Sung BJ, Yethiraj A. Sequence dependent self-assembly of beta-peptides: Insights from a coarse-grained model. The Journal of Chemical Physics. 132: 065103. PMID 20151759 DOI: 10.1063/1.3314309  0.668
2010 Mondal J, Zhu X, Cui Q, Yethiraj A. Self-assembly of β-Peptides: Insight from the pair and many-body free energy of association Journal of Physical Chemistry C. 114: 13551-13556. DOI: 10.1021/Jp1040772  0.553
2009 Mondal J, Sung BJ, Yethiraj A. Sequence-directed organization of beta-peptides in self-assembled monolayers. The Journal of Physical Chemistry. B. 113: 9379-85. PMID 19545127 DOI: 10.1021/Jp903341U  0.661
Show low-probability matches.