De-Sheng Ker
@kerds.bsky.social
Study marcomolecules at atomic details.
Optimistic realist.
The road less taken.
Celebrate failures.
Reverse Midas Hands.
Optimistic realist.
The road less taken.
Celebrate failures.
Reverse Midas Hands.
Pinned
Better and faster microscope generates large amount of data which then lead to high resolution image. With AI server hunger for more data storage too, look like data storage will be next bottleneck in image processing.
Still this is pale in comparison with data generated by LHC per day.
Still this is pale in comparison with data generated by LHC per day.
Hard drives on backorder for two years as AI data centers trigger HDD shortage — delays forcing rapid transition to QLC SSDs
The AI boom might help QLC overtake TLC in the next two years.
www.tomshardware.com
November 14, 2025 at 10:42 PM
Better and faster microscope generates large amount of data which then lead to high resolution image. With AI server hunger for more data storage too, look like data storage will be next bottleneck in image processing.
Still this is pale in comparison with data generated by LHC per day.
Still this is pale in comparison with data generated by LHC per day.
Reposted by De-Sheng Ker
This ‘landmark’ study describes the structural mechanism of strand exchange by the RAD51 filament using cryogenic structural, biochemical, and single-molecule analyses.
buff.ly/Ieh84gj
buff.ly/Ieh84gj
August 26, 2025 at 10:02 AM
This ‘landmark’ study describes the structural mechanism of strand exchange by the RAD51 filament using cryogenic structural, biochemical, and single-molecule analyses.
buff.ly/Ieh84gj
buff.ly/Ieh84gj
Reposted by De-Sheng Ker
Over five years of work has gone into our new preprint! The #cryoEM structure of a human RAD51 filament caught at the point of strand exchange 🧬
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Structural mechanism of strand exchange by the RAD51 filament.
Homologous Recombination (HR) preserves genomic stability by repairing double-strand DNA breaks and ensuring efficient DNA replication. Central to HR is the strand-exchange reaction taking place within the three-stranded synapsis wherein a RAD51 nucleoprotein filament binds to a donor DNA. Here we present the cryoEM structure of a displacement loop of human RAD51 that captures the synaptic state when the filament has become tightly bound to the donor DNA. The structure elucidates the mechanism of strand exchange by RAD51, including the filament engagement with the donor DNA, the strand invasion and pairing with the complementary sequence of the donor DNA, the capture of the non-complementary strand and the polarity of the strand-exchange reaction. Our findings provide fundamental mechanistic insights into the biochemical reaction of eukaryotic HR. ### Competing Interest Statement The authors have declared no competing interest.
www.biorxiv.org
March 27, 2025 at 3:12 PM
Over five years of work has gone into our new preprint! The #cryoEM structure of a human RAD51 filament caught at the point of strand exchange 🧬
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
TIL, New Zealand allows direct prescription drug advertising to consumer.
February 22, 2025 at 11:18 PM
TIL, New Zealand allows direct prescription drug advertising to consumer.
Reposted by De-Sheng Ker
Join the first Keystone conference dedicated to DNA replication gaps and cancer! Send an abstract to be selected for a talk.
www.keystonesymposia.org/conferences/...
www.keystonesymposia.org/conferences/...
DNA Replication Gaps, Cancer and Disease | Keystone Symposia
Join us at the Keystone Symposia on DNA Replication Gaps, Cancer and Disease, April 2025, in Daejeon, with field leaders!
www.keystonesymposia.org
January 17, 2025 at 11:35 AM
Join the first Keystone conference dedicated to DNA replication gaps and cancer! Send an abstract to be selected for a talk.
www.keystonesymposia.org/conferences/...
www.keystonesymposia.org/conferences/...
Just only discover the "--reuse_scratch" and "--keep_scratch" option in RELION, to minimize repetitively copying the same particle set into the cache directory for each job. I should have read more carefully at the long list of command options available.
October 5, 2024 at 10:49 AM
Just only discover the "--reuse_scratch" and "--keep_scratch" option in RELION, to minimize repetitively copying the same particle set into the cache directory for each job. I should have read more carefully at the long list of command options available.
Mastering the act to remotely wake up a workplace Linux machine from sleep using a smartphone at home with a single click.
By putting PC to sleep, is estimated to reduce the machine's power consumption by ten times when compared to its idle power consumption.
By putting PC to sleep, is estimated to reduce the machine's power consumption by ten times when compared to its idle power consumption.
June 1, 2024 at 10:08 AM
Mastering the act to remotely wake up a workplace Linux machine from sleep using a smartphone at home with a single click.
By putting PC to sleep, is estimated to reduce the machine's power consumption by ten times when compared to its idle power consumption.
By putting PC to sleep, is estimated to reduce the machine's power consumption by ten times when compared to its idle power consumption.
Source code available; easy to install; run test dataset without error; and job finish in less than a minute. 🤯
But it using a non-standard input and output format which require installation of additional software 😫
But it using a non-standard input and output format which require installation of additional software 😫
Graphormer/distributional_graphormer/protein at dig-v1.0 · microsoft/Graphormer
Graphormer is a general-purpose deep learning backbone for molecular modeling. - microsoft/Graphormer
github.com
May 27, 2024 at 6:28 PM
Source code available; easy to install; run test dataset without error; and job finish in less than a minute. 🤯
But it using a non-standard input and output format which require installation of additional software 😫
But it using a non-standard input and output format which require installation of additional software 😫
cryoSPARC benchmark of some GPU workstation in the department
April 11, 2024 at 7:57 AM
cryoSPARC benchmark of some GPU workstation in the department
mamba is faster than conda 🐍
March 14, 2024 at 4:39 PM
mamba is faster than conda 🐍
Spent 1 hours trying to install a software, spent another 3 hours trying to work out how to use the software (poor documentation), only for the job to quit with an error: CUDA out of memory. 🥲
March 13, 2024 at 8:33 PM
Spent 1 hours trying to install a software, spent another 3 hours trying to work out how to use the software (poor documentation), only for the job to quit with an error: CUDA out of memory. 🥲
So it is possible to finish the RELION 2D classification with EM after VDAM using additional argument "--grad_em_iters 25"
March 9, 2024 at 9:51 AM
So it is possible to finish the RELION 2D classification with EM after VDAM using additional argument "--grad_em_iters 25"
Most cryoEM lab workstation: AMD ThreadRipper + 4090
Me: Ryzen 9 + 4070 Ti Super
Me: Ryzen 9 + 4070 Ti Super
March 3, 2024 at 6:53 PM
Most cryoEM lab workstation: AMD ThreadRipper + 4090
Me: Ryzen 9 + 4070 Ti Super
Me: Ryzen 9 + 4070 Ti Super
February 21, 2024 at 7:44 PM
Interesting,
(1xMPI, 64 Threads, --cpu) RELION's VDAM rans faster than (1xMPI, 32 Threads, 1 GPU, --gpu) RELION's VDAM in our HPC.
Also execute RELION's VRAM command with either mpirun or mpiexec are significant slower than srun command.
(1xMPI, 64 Threads, --cpu) RELION's VDAM rans faster than (1xMPI, 32 Threads, 1 GPU, --gpu) RELION's VDAM in our HPC.
Also execute RELION's VRAM command with either mpirun or mpiexec are significant slower than srun command.
December 13, 2023 at 7:08 PM
Interesting,
(1xMPI, 64 Threads, --cpu) RELION's VDAM rans faster than (1xMPI, 32 Threads, 1 GPU, --gpu) RELION's VDAM in our HPC.
Also execute RELION's VRAM command with either mpirun or mpiexec are significant slower than srun command.
(1xMPI, 64 Threads, --cpu) RELION's VDAM rans faster than (1xMPI, 32 Threads, 1 GPU, --gpu) RELION's VDAM in our HPC.
Also execute RELION's VRAM command with either mpirun or mpiexec are significant slower than srun command.
From Blue Letter F to Blue Birds, now to Blue Sky.
December 12, 2023 at 11:17 PM
From Blue Letter F to Blue Birds, now to Blue Sky.