Computational chemist | Assistant professor | I tweet about research.| #compchem
Joined March 2021
- Tweets 471
- Following 101
- Followers 136
- Likes 882
18 Photos and videos
Pinned Tweet
1 Feb 2023
#compchem
Read my latest review article, published with @SpringerNature in @BiophysicalRev1
"Free energy andkinetic rate calculation via non‑equilibrium molecular simulation: application tobiomolecules"
Read here: rdcu.be/c4BBD
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- "ff14SB and ff19SB, have been ported to GROMACS as AMBER14SB and AMBER19SB."
- "Experimental support for H5MD as a trajectory output format for mdrun."
manual.gromacs.org/2026.0/re…
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Specific protein-RNA interactions are mostly preserved in biomolecular condensates | Science Advances science.org/doi/10.1126/scia…
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20 Feb 2024
A Reference Data Set for Circular Dichroism Spectroscopy Comprised of Validated Intrinsically Disordered Protein Models
biorxiv.org/content/10.1101/…
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shinji iida retweeted
10 Feb 2024
Any @mdanalysis users at #BPS2024 - come find me to get your hands on some shiny MDAnalysis stickers - now featuring a small selection of cat-based stickers! Look for the pink hair, or come by my poster B374 on Tuesday and also hear about my work with sugar transporters
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31 Jan 2024
Polarizable AMOEBA Model for Simulating Mg2 ·Protein·Nucleotide Complexes | Journal of Chemical Information and Modeling pubs.acs.org/doi/10.1021/acs…
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15 Jan 2024
#compchem
His fantastic MD-based method (Multicanonical) is able to see accurate binding poses on an RNA as well. I've always learnt a lot.
Binding Mechanism of Riboswitch to Natural Ligand Elucidated by McMD-Based Dynamic Docking Simulations | ACS Omega pubs.acs.org/doi/full/10.102…
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Sequence-Dependent Conformational Transitions of Disordered Proteins During Condensation biorxiv.org/content/10.1101/…
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5 Jan 2024
Block averaging is used to reduce autocorrelation in a trajectory of non-i.i.d. random variables, thereby producing a set of block averages independent.
Using block averages to calculate statistical errors in estimates of the... youtu.be/0KqCK0yG9T0?si=F8ET… via @YouTube
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shinji iida retweeted
14 Dec 2023
AlphaFold2 has more to learn about protein energy landscapes biorxiv.org/cgi/content/shor… #biorxiv_bioinfo
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shinji iida retweeted
13 Dec 2023
I'll be presenting my (spotlight) paper "Accelerating Inference in Molecular Diffusion Models with Latent Representations of Protein Structure" at the #NeurIPS23 @genbio_workshop. Stop by or reach out to me if you want to chat before then! openreview.net/forum?id=Z4ia…
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14 Dec 2023
Intriguing recap.
Space exploration: finding new protein conformations using AlphaFold2
nature.com/articles/s41594-0…
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shinji iida retweeted
12 Dec 2023
Please RT! The #ISQBP2024 President's meeting will take place 19-23 May in Athens, Greece!
We are now accepting abstract submissions for oral and poster presentations: isqbp2024.org
Early-bird registration: 1 February 2023
Looking forward to welcoming all in Athens!
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11 Dec 2023
Force Field Analysis Software and Tools (FFAST): Assessing Machine Learning Force Fields under the Microscope | Journal of Chemical Theory and Computation pubs.acs.org/doi/10.1021/acs…
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Investigation of Rare Protein Conformational Transitions via Dissipation-Corrected Targeted Molecular Dynamics | Journal of Chemical Theory and Computation pubs.acs.org/doi/10.1021/acs…
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shinji iida retweeted
1 Dec 2023
Important for those who use GROMACS. pubs.acs.org/doi/10.1021/acs…
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29 Nov 2023
I have a chat with Gisbert in the chemoinformatics autumn school in Japan, and he always encourages me to make progress for my research 😊
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shinji iida retweeted
29 Oct 2023
I am delighted to announce publication of the 4th edition of Linear Algebra Done Right as an Open Access book. The electronic version is legally free to the world at linear.axler.net/.
That website also has links to pre-order the print version of the book.
#linearalgebra
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