Inquiry regarding TM-Score, TM-Align, and 3DRobot
Posted: Thu Jun 22, 2023 1:24 am
Hello,
I hope this email finds you well.
I am writing to inquire about a few questions regarding the tools provided by Zhang Lab, specifically the TM-Score, TM-Align, and 3DRobot. I have encountered some observations and would greatly appreciate your assistance in clarifying these matters.
Q1: Discrepancy between TM-Align and TM-Score results
While utilizing both TM-Align and TM-Score to assess the structural similarity between an AlphaFold2 model and the true structure, I noticed that TM-Align yields slightly lower TM scores compared to the TM-Score server. I am curious to understand the reasons behind this disparity.
Q2: RMSD calculation and its correlation to structural proximity
Upon utilizing TM-Align and evaluating the Root Mean Square Deviation (RMSD), I observed low RMSD scores indicating "Good" alignment, despite the structure not being particularly close to the true structure. I would appreciate an explanation regarding how RMSD is calculated and why it may not always reflect structural proximity accurately.
Q3: Discrepancy in the number of decoys generated by 3DRobot
When submitting a job using 3DRobot and specifying a request for 1000 decoys, I received an output with only 308 decoys. I am interested in understanding the factors contributing to this discrepancy and why the requested number of decoys was not fully generated.
Thank you for your time and attention to these inquiries. I greatly value the expertise of Zhang Lab and look forward to your insights.
Best regards,
MNA
I hope this email finds you well.
I am writing to inquire about a few questions regarding the tools provided by Zhang Lab, specifically the TM-Score, TM-Align, and 3DRobot. I have encountered some observations and would greatly appreciate your assistance in clarifying these matters.
Q1: Discrepancy between TM-Align and TM-Score results
While utilizing both TM-Align and TM-Score to assess the structural similarity between an AlphaFold2 model and the true structure, I noticed that TM-Align yields slightly lower TM scores compared to the TM-Score server. I am curious to understand the reasons behind this disparity.
Q2: RMSD calculation and its correlation to structural proximity
Upon utilizing TM-Align and evaluating the Root Mean Square Deviation (RMSD), I observed low RMSD scores indicating "Good" alignment, despite the structure not being particularly close to the true structure. I would appreciate an explanation regarding how RMSD is calculated and why it may not always reflect structural proximity accurately.
Q3: Discrepancy in the number of decoys generated by 3DRobot
When submitting a job using 3DRobot and specifying a request for 1000 decoys, I received an output with only 308 decoys. I am interested in understanding the factors contributing to this discrepancy and why the requested number of decoys was not fully generated.
Thank you for your time and attention to these inquiries. I greatly value the expertise of Zhang Lab and look forward to your insights.
Best regards,
MNA