Dheeraj Kumar Sarkar
@Dheeraj_Sarkar_
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Postdoctoral Fellow, TIFR Hyderabad | computational biophysics | ligand transport processes
Hyderabad
Joined December 2018
RT @MandalNishita: Excited to share our research with @surpeta_b and @JanBrezovsky1, recently published in JCIM @JCIM_JCTC! .We explored ra….
pubs.acs.org
Tunnels are structural conduits in biomolecules responsible for transporting chemical compounds and solvent molecules from the active site. They have been shown to be present in a wide variety of...
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Happy to share our recent work in @jctc_papers with prof. @JanBrezovsky1 and @surpeta_b. We explored the role of prior knowledge in high-throughput molecular dynamics simulations to better capture the nuances of ligand transport processes. More details:
pubs.acs.org
Because most proteins have buried active sites, protein tunnels or channels play a crucial role in the transport of small molecules into buried cavities for enzymatic catalysis. Tunnels can critica...
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RT @MandalNishita: Happy to share our latest preprint in enzyme tunnel exploration with @surpeta_b and @JanBrezovsky1. We delved into hidd….
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RT @JanBrezovsky1: Water traveling into unexpected reaches of empty voids in proteins. #Bioinformatics #Biochemistry.
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RT @dmtapu: Suitability of Adenosine Derivatives in Improving the Activity and Stability of Cytochrome c under Stress: Insights into the Ef….
pubs.acs.org
It is well known that adenosine and its phosphate derivatives play a crucial role in biological phenomena such as apoptosis and cell signaling and act as the energy currency of the cell. Although...
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Congratulations 🎊.
Super excited to share that our project to study coarse grained tunnels in collaboration with @CG_Martini has qualified for funding through very competitive #PRELUDIUM22 grant by the @NCN_PL 😍. Only 10.7% accepted this year!.Special thanks to my PI @JanBrezovsky1 and @UAM_IBMiB
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Check out our new preprint with @surpeta_b and @JanBrezovsky1 on knowledge infused seedings in high-throughput simulations for precise understanding of ligand transport and kinetics. @UAM_IBMiB @IIMCB_Poland.
Incorporating prior knowledge to seeds of adaptive sampling molecular dynamics simulations of ligand transport in enzymes with buried active sites #bioRxiv.
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I'm pleased to share that our work together with @JanBrezovsky1 and @dmtapu is published in Green Chemistry @green_rsc. Herein, we discussed the effects of co-hydrotropic solvents on the stability and activity of Cytochrome c. @IIMCB_Poland, @UAM_IBMiB.
pubs.rsc.org
Green and nano-structured catalytic media are vital for biocatalysis to attenuate the denaturation tendency of biocatalysts under severe reaction conditions. Hydrotropes with multi-faceted physioch...
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It was a good time in Toulouse, France, to present my work on "Hydrotropic solvent effects on Cytochrome c dynamics and function" at #GGMM23 (for Young Modellers)
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RT @surpeta_b: I am pleased to announce that, together with @JanBrezovsky1 , we designed the first set of penicillin G acylase variants tun….
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RT @JanBrezovsky1: Our manuscript about molecular mechanisms behind the unique selectivity of a plant ABCG46 transporter, which is so unlik….
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RT @JanBrezovsky1: Here tou can see molecular details on how hydrotropes can mobilize functional dynamics of cytochrome c at one hand while….
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Check out our new preprint on improved protein packing and bio catalysis in harsh environments with @JanBrezovsky1 and @dmtapu. We proposed a strategy to protect mitochondrial cells from ROS-triggered apoptosis. #bioRxiv.
biorxiv.org
Green and nanostructured catalytic media are vital in biocatalysis to attenuate the denaturation tendency of biocatalysts under severe reaction conditions. Hydrotropes with multifaceted physiochemi...
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RT @JanBrezovsky1: This is also very neat way of keeping the details on all the tunnels calculated in each simulation snapshot without havi….
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RT @surpeta_b: Check out the newest implementation released by @carseq in @JanBrezovsky1 lab! This approach will help you to use resources….
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RT @carseq: Interested in protein 𝘁𝘂𝗻𝗻𝗲𝗹𝘀 𝗶𝗻 𝗹𝗼𝗻𝗴 𝗠𝗗 𝘀𝗶𝗺𝘂𝗹𝗮𝘁𝗶𝗼𝗻𝘀? If so, our recently published paper at @JanBrezovsky1 lab can help you. O….
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RT @anunesalves: Pls RT!.I have one open PhD position in Berlin @unisyscat to model and simulate the effects of crowded cell-like environme….
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RT @JanBrezovsky1: We have a postdoc position available. Come help us unveil how ligand transport affects enzymatic action through state-of….
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RT @IIMCB_Poland: Scientists from the @IIMCB_Poland, led by @JanBrezovsky1 Ph.D., have recently published a paper entitled „Common Dynamic….
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RT @anunesalves: Huge welcome to my first PhD student, @Farzin72256221, and to @Dheeraj58194038, who will visit my lab for a month. There w….
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