User: Nestor Wendt

gravatar for Nestor Wendt
Nestor Wendt100
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100
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Brazil
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15 hours ago
Joined:
5 years, 8 months ago
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n**********@gmail.com

Posts by Nestor Wendt

<prev • 15 results • page 1 of 2 • next >
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Answer: A: Dear biostars I really need your kindly help, please save me from this hardship
... There are some docker containers for [mirdeep2][1]. [1]: https://hub.docker.com/search/?isAutomated=0&isOfficial=0&page=1&pullCount=0&q=mirdeep2&starCount=0 ...
written 3.8 years ago by Nestor Wendt100
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Answer: A: Which programs generate good images of structural biology models or molecular dy
... You can try [UCSF Chimera][1]. [1]: https://www.cgl.ucsf.edu/chimera/ ...
written 4.0 years ago by Nestor Wendt100
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Comment: C: Molecular Dynamics in Acetic Acid
... You can use [PRODRG][1] to generate the topology, as they did [here][2]. [1]: http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg [2]: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019830#s3 ...
written 4.0 years ago by Nestor Wendt100
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Comment: C: Molecular Dynamics in Acetic Acid
... > I calculate that given the box type I choose right? (if I choose rhombic dod and I need 20% AA I just need to make calculations, correct me if I'm wrong) Not only the box type. The -d option of [gmx editconf][1] changes the box size as well. The stdout output from gmx editconf shows you the bo ...
written 4.0 years ago by Nestor Wendt100
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Comment: C: Molecular Dynamics in Acetic Acid
... Take a look at [http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents][1] [1]: http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents ...
written 4.1 years ago by Nestor Wendt100
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Answer: A: Help using BUSCO to assess quality of transcriptome
... Hello, I ran into this problem yesterday but could not figure it out. However, when I tried running BUSCO from [this][1] Docker container, it worked. Once you have Docker installed, just run something like that: docker run -v /path/to/workdir/:/input -v /path/to/workdir/:/results cfriedline/bu ...
written 4.3 years ago by Nestor Wendt100
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Comment: C: protein structure modeling
... [SWISS-MODEL][1] is good and user-friendly. [1]: http://swissmodel.expasy.org/ ...
written 4.4 years ago by Nestor Wendt100
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Answer: A: How to predict Protein-Protein Interactions from a pair of gene symbols?
... First, I would try to find an entry at PDB for the genes you have. I suppose you have (or can obtain) the sequences for these genes. Note that one gene can have several isoforms. To do that, a simple blastx or blastp search in the PDB database is enough. That can be done through the NCBI BLAST. Look ...
written 4.5 years ago by Nestor Wendt100 • updated 7 months ago by RamRS28k
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Answer: A: Downloading multiple PDB sequences
... You can download PDB sequences directly from the website: http://www.rcsb.org/pdb/download/download.do#FASTA ...
written 4.7 years ago by Nestor Wendt100 • updated 8 months ago by RamRS28k
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Answer: A: Disrupted protein structure after 5 nanoseconds of GROMACS molecular dynamics
... For those who encounter this problem in the future. After converting the trajectory file (.trr) to (.xtc) using `gmx trjconv` with the following parameter `-pbc nojump`, these jumps stop appearing. This tutorial called this jumps 'pdc artifacts', and there, before visual analysis they were removed. ...
written 4.9 years ago by Nestor Wendt100 • updated 8 months ago by RamRS28k

Latest awards to Nestor Wendt

Popular Question 2.8 years ago, created a question with more than 1,000 views. For Disrupted protein structure after 5 nanoseconds of GROMACS molecular dynamics
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Effects of random hexamer priming bias in RNA-Seq de novo assembly
Student 5.3 years ago, asked a question with at least 3 up-votes. For Effects of random hexamer priming bias in RNA-Seq de novo assembly

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