User: jgreener

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jgreener220
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Posts by jgreener

<prev • 22 results • page 1 of 3 • next >
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Comment: C: splitting test and train data
... If you are splitting proteins into a training and test set you also want to eliminate pairs of homologous proteins across the training/test set, otherwise you might just end up learning how to recognise homology. As an absolute minimum there shouldn't be any sequences in the test set with >30% se ...
written 3 days ago by jgreener220
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Answer: A: Get real model numbers from PDB using BioPython
... Yes, you can use the property "model.serial_num" to get the model number that was actually in the file (with no off-by-one shift), though I'm not sure this is documented anywhere. See https://github.com/biopython/biopython/blob/master/Bio/PDB/PDBParser.py#L326-L334 and https://github.com/biopython/ ...
written 24 days ago by jgreener220
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Comment: C: Predict protein secondary structure from alignment
... Does B mean either aspartic acid or asparagine? If so, you could replace B with D or N and run through PSIPRED. ...
written 24 days ago by jgreener220
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Comment: C: Residues in contact with ligands in PDB files
... You could find it programmatically by finding the first residue with the desired residue name: allres = collectresidues(struc) fmnres = allres[findfirst(r -> resname(r) == "FMN", allres)] Yes, 4 is for 4 Angstrom. I just chose it as a distance below which atoms could be considered as co ...
written 25 days ago by jgreener220
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Answer: A: Residues in contact with ligands in PDB files
... Yes, you can use the information in STRUCT_SITE_GEN listed under AC1 to get the binding residues: TYR24, TYR25, ALA76 etc. If you did want to do this from the coordinate data, one way would be to use [BioStructures.jl][1] in Julia: using BioStructures struc = read("1AL7.cif", MMCIF) re ...
written 4 weeks ago by jgreener220
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Comment: C: Problem in 3D modelling of ALSIN protein
... I'm afraid I can't solve all your problems for you, but I would recommend MODELLER for stitching together different models. If you suspect the model will be rubbish then don't put it in your article, just show the domains separately. ...
written 8 weeks ago by jgreener220
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Comment: C: Problem in 3D modelling of ALSIN protein
... Yes, I would broadly agree, getting the fold right is hard enough let alone predicting the effects of variants. There has been surprisingly little work in assessing the utility of de novo models for variant effect prediction, but it is something we are working on. I wouldn't expect individual struc ...
written 8 weeks ago by jgreener220
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Comment: C: Problem in 3D modelling using SWISS-MODEL
... > Are you familiar with any good training source for molecular dynamic simulation specially with GROMACS? I have found these tutorials useful: http://www.mdtutorials.com/gmx/ ...
written 8 weeks ago by jgreener220
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Answer: A: Problem in 3D modelling of ALSIN protein
... If you are trying to model a protein without an available template you could try our method DMPfold, which is available as a web server [here][1] and described in [this paper][2]. Template-free modelling has improved considerably in the last few years, but just submitting a 1500+ residue protein is ...
written 8 weeks ago by jgreener220
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Answer: A: What are some areas where machine learning is applicable in biology and cancer?
... To add to the other answers, machine learning and in particular deep neural networks have revolutionised the field of protein structure prediction. See some (slightly over-hyped) press coverage at https://www.theguardian.com/science/2018/dec/02/google-deepminds-ai-program-alphafold-predicts-3d-shape ...
written 3 months ago by jgreener220

Latest awards to jgreener

Supporter 7 days ago, voted at least 25 times.
Scholar 21 days ago, created an answer that has been accepted. For A: Evaluating protein structure predictions
Scholar 29 days ago, created an answer that has been accepted. For A: Evaluating protein structure predictions
Scholar 8 months ago, created an answer that has been accepted. For A: Evaluating protein structure predictions
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Evaluating protein structure predictions
Scholar 9 months ago, created an answer that has been accepted. For A: Evaluating protein structure predictions
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Evaluating protein structure predictions

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