Questions tagged [protein-structure]
The 3-D structure of a protein in space. It can refer to secondary structures, such as alpha helices or beta sheets, or the 3-D coordinates of the atoms making up a protein.
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How can I visualize protein secondary structure?
I'm currently working on a secondary structure prediction model and I'd like to visualize what will be predicted , the format of secondary structure sequence is consisted of 8 labels:
G: 3-turn helix ...
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LigPlot (LigPlus) Giving Different Interactions on Command Line and GUI
I am trying to determine the interaction of the targeted amino acid with other amino acids, but I am having trouble. When I pass a PDB file of a protein that has ligands, I can see the interactions. ...
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Is there a way to download all data containing amino acid sequence - secondary protein structure from protein data bank
Is there a way to download all data containing amino acid sequence - secondary protein structure from protein data bank(https://www.rcsb.org/).
Or is there a way to extract the data programaticaly ...
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Low confidence score from alphafold2_multimer_v3
I am running alphafold2_multimer_v3 in ColabPro (A100 40 GB GPU) with the following parameters:
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Is there any standardized and ready-to-use dataset available online for download regarding protein geometry? [closed]
I want to do ML model training and data analysis for secondary structure prediction.
Is there any standardized and ready-to-use dataset available online regarding protein geometry?
For example, the ...
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How can I detect secondary structures in a protein using a hydrogen bond detection algorithm?
Suppose I have a protein chain. And I have a hydrogen bond detection algorithm that can detect hydrogen bonds in a protein chain. Say, the name of the algorithm is HBDA algorithm.
How can I detect ...
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How to create a dataset of contact maps of homologous proteins?
Disclaimer: I am a machine learning researcher working on network science and want to use proteins to test an algorithm of mine using real-world data. My bioinformatics knowledge is minimal.
I need to ...
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Method for reproducing minimal, cartoon-style protein structure visualisation
I recently came across a preprint ( DOI, PDF link ) that has some figures of protein structures in a style that I have not seen before. To me it appears easier on the eyes and less noisy than the ...
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Protein symmetry classification from PDB data
Given the PDB or mmCIF information of a homomeric protein assembly whose global symmetry is unknown, how might one design an algorithm to find which point group symmetry class it belongs to (cyclic $...
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Tools and software to visualize the moving cell compartments in 3D
Also asked on biostars
I am looking for tools and software that could help me visualize moving cell compartments in 3D where I can go from the cell membrane to the ER, then out with the protein into ...
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Oligomer status prediction with Alphafold 2
I am new to using Alphafold 2 and have been primarily using ChimeraX and Colabfold to run some preliminary predictions.
I am particularly interested in using AF2 to predict the homo-oligomerization ...
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Q8 Accuracy Evaluation metric mathematical expression used in Protein Secondary Structure Prediction
I am working on Protein Secondary Structure Prediction using Recurrent Neural Network (GRU) model. I came across few open source projects which already worked on the similar problem. All of them are ...
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Best Library for 3D Protein Structure Visualization and Annotation
I have a background in Computer Science and have recently gotten very interested in the field of Protein Engineering. I am trying to build a web app which displays the 3D structure of a protein when I ...
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Energy error margin for protein structures
I would like to know the acceptable error margin for the lowest free energy of a protein. In other words, say, both Group A and B have determined the lowest free energy of the same protein in their ...
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Does AlphaFold actually calculates the fold?
After reading through papers and the code, I'm still not clear if AlphaFold and the likes do actually calculate the 3d structure. My current feeling they are more like information retrieval engines. ...
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