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 |
0.689 |
|
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 |
0.714 |
|
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 |
|
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