User: Nestor Wendt

gravatar for Nestor Wendt
Nestor Wendt100
Reputation:
100
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Trusted
Location:
Brazil
Last seen:
2 months, 3 weeks ago
Joined:
4 years, 9 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 2.9 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 3.1 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 3.1 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 3.2 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 3.2 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 3.4 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 3.5 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 3.6 years ago by Nestor Wendt100
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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 3.8 years ago by Nestor Wendt100
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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 4.0 years ago by Nestor Wendt100

Latest awards to Nestor Wendt

Popular Question 23 months ago, created a question with more than 1,000 views. For Disrupted protein structure after 5 nanoseconds of GROMACS molecular dynamics
Popular Question 3.4 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 4.4 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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