Osvaldo Burastero
@osvalb.bsky.social
Biophysics enthusiast. Currently focused on data analysis: https://spc.embl-hamburg.de
Reposted by Osvaldo Burastero
Curious fact: many researchers normalise the CD signal using the number of residues. Others, use the number of peptide bonds. Still, everyone calls it 'mean residue molar ellipticity/extinction'. The cromophore unit is the peptide bond, so use that. For short peptides, it matters. 👍
January 31, 2025 at 10:58 AM
Curious fact: many researchers normalise the CD signal using the number of residues. Others, use the number of peptide bonds. Still, everyone calls it 'mean residue molar ellipticity/extinction'. The cromophore unit is the peptide bond, so use that. For short peptides, it matters. 👍
The estimated Kd (micromolar) is 1.3, and we also provide the asymmetric confidence interval: [0.5 - 3.1] (link.springer.com/article/10.1...)
The reported Kd by the authors was 1.2.
6. Extra: I scaled the plot to start around 0.
The reported Kd by the authors was 1.2.
6. Extra: I scaled the plot to start around 0.
January 31, 2025 at 10:24 AM
The estimated Kd (micromolar) is 1.3, and we also provide the asymmetric confidence interval: [0.5 - 3.1] (link.springer.com/article/10.1...)
The reported Kd by the authors was 1.2.
6. Extra: I scaled the plot to start around 0.
The reported Kd by the authors was 1.2.
6. Extra: I scaled the plot to start around 0.
4. Go to the '2. Fitting' section. Inside the 'Advanced settings', set the Kd max value to 5 micromolar (to help the fitting algorithm 😄😬 ).
5. Press on 'Run fitting' and voila!
5. Press on 'Run fitting' and voila!
January 31, 2025 at 10:24 AM
4. Go to the '2. Fitting' section. Inside the 'Advanced settings', set the Kd max value to 5 micromolar (to help the fitting algorithm 😄😬 ).
5. Press on 'Run fitting' and voila!
5. Press on 'Run fitting' and voila!
2. Import the file into our tool ThermoAffinity (spc.embl-hamburg.de/app/thermoAf...)
3. Set the units to 'Nanomolar' and the hot region between 14 - 20 seconds (based on what the authors reported)
3. Set the units to 'Nanomolar' and the hot region between 14 - 20 seconds (based on what the authors reported)
January 31, 2025 at 10:24 AM
2. Import the file into our tool ThermoAffinity (spc.embl-hamburg.de/app/thermoAf...)
3. Set the units to 'Nanomolar' and the hot region between 14 - 20 seconds (based on what the authors reported)
3. Set the units to 'Nanomolar' and the hot region between 14 - 20 seconds (based on what the authors reported)
Hope this makes it easier to reproduce published analyses. A short example (circa 10 minutes):
1. Downloaded the microscale thermophoresis raw data Lys VHH B09 25 nM Lys100uM max_MSTTraceRawData.xlsx, available at
mbdb-data.org/mst/5s81t-w6...
1. Downloaded the microscale thermophoresis raw data Lys VHH B09 25 nM Lys100uM max_MSTTraceRawData.xlsx, available at
mbdb-data.org/mst/5s81t-w6...
Molecular Biophysics Database
mbdb-data.org
January 31, 2025 at 10:24 AM
Hope this makes it easier to reproduce published analyses. A short example (circa 10 minutes):
1. Downloaded the microscale thermophoresis raw data Lys VHH B09 25 nM Lys100uM max_MSTTraceRawData.xlsx, available at
mbdb-data.org/mst/5s81t-w6...
1. Downloaded the microscale thermophoresis raw data Lys VHH B09 25 nM Lys100uM max_MSTTraceRawData.xlsx, available at
mbdb-data.org/mst/5s81t-w6...