@SamikBose2

Comp Chem/Biophysics postdoc @michiganstateu @MSU_NatSci. Alumni of @SXC_Kol, @HydUniv, @csir_ncl and @iacskolkata. Love to sit in front of a computer 24X7.

 East Lansing, MI
Joined July 2020
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Interested in exploring kinetics of biomolecular systems at min/hours timescale? Please have a read: pubs.acs.org/doi/10.1021/acs… My first lead-author paper since joining CMSE dept at MSU. Thanks to @dicksonlab and @ccerenkilinc for the brainstorming sessions.

Markov State Models with Weighted Ensemble Simulation: How to Eliminate the Trajectory Merging Bias

Abstract. The weighted ensemble (WE) algorithm is gaining popularity as a rare event method for studying long timescale processes with molecular dynamics.

pubs.acs.org
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3. We propose an analytical solution for the problem with merging bias corrected MSMs. 4. At higher lag-time, MBC-MSM provides statistically significant and accurate prediction of rates for an inhibitor unbinding from soluble epoxide hydrolase protein with MFPT of ~27 min!!
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Key points: 1. Standalone Weighted Ensemble estimated rates (at min/hrs range) are noisy. 2. Integrating WE with history augmented MSM provides significant gain in accuracy/robustness, but runs into the problem of 'merging bias', which is key in the success of any WE strategy.
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Cheers to yet another achievement @GhoshDebashree1! Congratulations to you and everyone at @QCLlab 🎉🎉
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Debashree Ghosh @GhoshDebashree1 will talk about "Photophysics of skin pigment melanin" #compchem ACS Science Talks: Virtual Lecture Series us02web.zoom.us/webinar/regi…
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Heading towards New Orleans with a lot of excitement! My first talk to a community outside COMP in the @ACS_BIOT ‘Emerging Biophysical Technology’ symposium on 19th followed by a WE-MSM talk in @ACSCOMP on 20th. In between I’ll preside a ML in Chem session too!! Please join us!!
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Anyone else mentally in New Orleans already? @ACSCOMP @ACS_BIOT @AmerChemSociety
American Chemical Society@AmerChemSociety3 Mar 2024
Flying into #NewOrleans for #ACSSpring2024? You can save time & hit the ground running by picking up your badge at the airport from March 15-17. Learn more about badge pick-up & on-site registration locations in New Orleans at brnw.ch/21wHwTt.
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Our work exploring the robustness of ligand binding transition state in the realm of kinetics driven drug design is out in @J_A_C_S. My 1st paper as lead author with @dicksonlab & it was an absolute pleasure! An interesting paper with technical details of REVO-MSM to follow soon!
J. Am. Chem. Soc.@J_A_C_S11 Nov 2023
How Robust Is the Ligand Binding Transition State? | Journal of the American Chemical Society @dicksonlab @michiganstateu @Ligand #Binding #TransitionState pubs.acs.org/doi/10.1021/jac…

How Robust Is the Ligand Binding Transition State?

Abstract. For many drug targets, it has been shown that the kinetics of drug binding (e.g., on rate and off rate) is more predictive of drug efficacy than

pubs.acs.org
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Alex has already explained the details of the work thoroughly in this tweet. Please have a read (the published version is of course more sound thanks to the reviewers), if you are interested in molecular modeling, in particular enhanced sampling MD or Markov state models.
Alex Dickson@dicksonlab23 Aug 2023
We have a 🚨new preprint🚨 out now examining ligand binding transition states for a set of five inhibitors of sEH! chemrxiv.org/engage/chemrxiv…
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What a shame @ScienceMagazine @GoogleDeepMind! This paper should never been accepted without code and model release! Perceived “Safety concern” is a total BS and very lame excuse!
Science Magazine
@ScienceMagazine19 Sep 2023
AlphaMissense, a tool by DeepMind, can help researchers learn more about the effects that missense mutations have on disease, and could help identify previously unknown disease-causing genes, according to a new Science study. Learn more: scim.ag/49l
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We are recruiting a postdoc in the lab. If you are interested in multiscale computational modeling, consider applying. sujobopps.com/postings/95844 Here is what we are up to acharyalab.com/ RT appreciated. #chempostdoc #compchem @SUChemistry @SUBioInspired @ArtSciencesSU
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Ligand binding transition states: what, why and how? I hope we have been able to answer a few key questions in the context of kinetics driven drug design. It’s my pleasure to continue working in the domain of ligand (un)binding kinetics! Many more to come!!
Alex Dickson@dicksonlab23 Aug 2023
We have a 🚨new preprint🚨 out now examining ligand binding transition states for a set of five inhibitors of sEH! chemrxiv.org/engage/chemrxiv…
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🚨We are hiring... Find more details about our work here : debashreeghosh.wixsite.com/d…

Research | Dglab

debashreeghosh.wixsite.com
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The ICQC in Bratislava has started. Here are the recent recipients of the annual IAQMS medal for scientists no older than 40 presented by the IAQMS President O. Eisenstein (right). From the left: S. Sharma, D. Ghosh, F. Evangelista, J. Toulouse, D. Zgid. Warmest congratulations!
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Here is Arpan's (@_arpan_Choudhry) super cool work hot off ChemRxiv: "Autonomous Assignment of Melanin Spectra amidst Dynamical Heterogeneity" doi.org/10.26434/chemrxiv-20… Happy to have contributed to this work with @GhoshDebashree1

Structure Prediction from Melanin Spectra amidst Dynamical Heterogeneity | ChemRxiv

Melanin is a biopolymer pigment that plays a central role in skin photoprotection. Its extensive chemical and dynamical heterogeneity impart this property through a broad featureless ultraviolet/vi...

chemrxiv.org
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My summary poem on singlet Fission for my TIFR colloquium that I gave yesterday @TIFRScience #sciencecomm 😍 tell me if you like it!
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Heal up @michiganstateu, it will take days to process the tragedy. I, my labmates and people whom I know in MSU are all safe but the mental scare will be tough to erase anytime soon! #MichiganStateUniversity
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This is fascinating indeed!!
Jagannath Mondal@Jmondal_tifrh10 Feb 2023
Published in @BiophysJ , we show long time-step MD simulation using Hydrogen Mass repartitioning scheme can actually slow down protein-ligand binding event, contrary to popular perception! sciencedirect.com/science/ar… Outstanding efforts by Sahil @msahil23 and Susmita @Ssumi96 1/2
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Nice postdoc opportunity (for #WomenInSTEM in India) to work with my PhD supervisor. Great science and even better people to work with! #compchem #biophysics #lifescience
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Is there a hack that we can do while compiling VMD which will enable us to start with user defined visual display settings rather than the default one (say I wanna set NewCartoon drawing method & white background color as default instead of the lines & black)?
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