User: João Rodrigues

gravatar for João Rodrigues
João Rodrigues2.5k
Reputation:
2,450
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Location:
Stanford University, U
Website:
http://www.github.com/...
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Last seen:
2 years, 3 months ago
Joined:
8 years, 9 months ago
Email:
j***************************@gmail.com

Computational Structural Biologist, focused on protein docking methodologies and in silico methods for structural studies.

Posts by João Rodrigues

<prev • 238 results • page 1 of 24 • next >
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Answer: A: merge pdb chains
... Try this: https://github.com/JoaoRodrigues/pdb-tools More specifically, this will extract chains A and B from your pdb, rename them to chain A, and renumber the residues sequentially from 1. ``` pdb_selchain.py -AB your.pdb | pdb_chain.py -A | pdb_reres.py -1 > new.pdb ``` ...
written 2.5 years ago by João Rodrigues2.5k
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Answer: A: mutation using PyMOL
... You would be better off using something like MODELLER, where you can then do a small restrained minimization of your mutated protein. In PyMOL, have a look at [this thread][1] of their mailing list. [1]: https://sourceforge.net/p/pymol/mailman/message/27979284/ ...
written 2.6 years ago by João Rodrigues2.5k
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Comment: C: Protein modelling with modeller
... MODELLER should build a structure of YOUR sequence using the structure you chose as a template and an alignment between YOUR sequence and the sequence of the template. If your model has a different sequence, something is wrong with your input.. ...
written 2.6 years ago by João Rodrigues2.5k
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Answer: A: Which programs generate good images of structural biology models or molecular dy
... Hi João, Have a look at the [Pymol Gallery][1]. As @genomax2 said, you are probably not using it correctly. You can import individual frames from your trajectory and work on an appropriate rendering style that you can then replicate for other frames/simulations. [1]: http://pymolwiki.org/index ...
written 2.6 years ago by João Rodrigues2.5k
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Answer: A: Homology modelling template
... Depends mostly on the sequence identity/similarity and the probability of it being a homologue. You can model human proteins from bacterial homologues. ...
written 2.8 years ago by João Rodrigues2.5k
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Answer: A: Is there any correlation between molecule sizes and their interaction energy aft
... Short answer: yes. The more atoms you have the more interactions you will have accounted for by the scoring function, therefore, the more 'energy' you will have. ...
written 2.8 years ago by João Rodrigues2.5k
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Answer: A: aligning a bound ligand from one PDB complex to a reference structure
... Hi there, Cross-posting from the Biopython mailing lists. Superimposer() will give you the rotation/translation matrix you need to superimpose the two structures. Then you just need to apply them selectively to the atoms you want (with Superimposer.apply). This script posted on [github][1] will ...
written 2.8 years ago by João Rodrigues2.5k
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Answer: A: Cartesian to internal coordinates (z-matrix representation)
... Have a look at OpenBabel: http://openbabel.org/wiki/Babel#File_Formats ...
written 3.8 years ago by João Rodrigues2.5k
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Answer: A: Beginner pymol user
... What your professor wants is for you to find all phosphorous atoms within a specific range (0-7Å) of an NZ or NH2 atoms of a Lys or Arg residue. Have a look at the Pymol wiki, namely the selection syntax and macros (e.g. within, around, byres, etc), an iterate. This should put you on your path to ge ...
written 3.9 years ago by João Rodrigues2.5k
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Comment: C: Missing segments of protein and minimization
... No. Besides the other answers, I pointed you to the HHpred website that does a pretty simple job at adding missing segments. You just need to learn the basics of homology modelling.  ...
written 3.9 years ago by João Rodrigues2.5k

Latest awards to João Rodrigues

Popular Question 2.6 years ago, created a question with more than 1,000 views. For pdb-tools: a set of Python scripts to manipulate PDB files.
Scholar 2.8 years ago, created an answer that has been accepted. For A: Protein Folding Trajectory Data
Appreciated 3.1 years ago, created a post with more than 5 votes. For A: C And Fortran Programming Language
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: State Of Biostar - Future Directions (January 2013)
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: Running Pymol From Python Script
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: Implementation Of Π-Π And Aromatic Interactions In Protein-Ligand Interactions
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: State Of Biostar - Future Directions (January 2013)
Scholar 3.9 years ago, created an answer that has been accepted. For A: Protein Folding Trajectory Data
Scholar 3.9 years ago, created an answer that has been accepted. For A: Protein Folding Trajectory Data
Scholar 3.9 years ago, created an answer that has been accepted. For A: Protein Folding Trajectory Data
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: State Of Biostar - Future Directions (January 2013)
Scholar 4.0 years ago, created an answer that has been accepted. For A: Protein Folding Trajectory Data
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: State Of Biostar - Future Directions (January 2013)
Scholar 4.0 years ago, created an answer that has been accepted. For A: Protein Folding Trajectory Data
Appreciated 4.0 years ago, created a post with more than 5 votes. For A: C And Fortran Programming Language
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: Surface Amino-Acid From Sequence Only
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: Implementation Of Π-Π And Aromatic Interactions In Protein-Ligand Interactions
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: Running Pymol From Python Script
Scholar 4.1 years ago, created an answer that has been accepted. For A: Protein Folding Trajectory Data
Scholar 4.2 years ago, created an answer that has been accepted. For A: Protein Folding Trajectory Data
Teacher 4.4 years ago, created an answer with at least 3 up-votes. For A: State Of Biostar - Future Directions (January 2013)
Scholar 4.5 years ago, created an answer that has been accepted. For A: Protein Folding Trajectory Data
Scholar 4.6 years ago, created an answer that has been accepted. For A: Protein Folding Trajectory Data
Teacher 4.6 years ago, created an answer with at least 3 up-votes. For A: State Of Biostar - Future Directions (January 2013)

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