openseq.org

OPENSEQ.org

GREMLIN is a method to learn a statistical model of a protein family that captures both conservation and co-evolution patterns in the family. The strength of measured co-evolution is strongly predictive of residue-residue contacts in the 3D structure of the protein. On this website, you can:. Submit contact prediction jobs for both monomers. Upload PDB models to see agreement to co-evolution data. Generate restraints to be used in Rosetta for modeling. We would also like to thank the developers of HHsuite.

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OPENSEQ.org | openseq.org Reviews

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GREMLIN is a method to learn a statistical model of a protein family that captures both conservation and co-evolution patterns in the family. The strength of measured co-evolution is strongly predictive of residue-residue contacts in the 3D structure of the protein. On this website, you can:. Submit contact prediction jobs for both monomers. Upload PDB models to see agreement to co-evolution data. Generate restraints to be used in Rosetta for modeling. We would also like to thank the developers of HHsuite.

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6 submissions casp12

7 downloads

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9 introduction

10 submit sequences

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OPENSEQ.org | openseq.org Reviews

https://openseq.org

GREMLIN is a method to learn a statistical model of a protein family that captures both conservation and co-evolution patterns in the family. The strength of measured co-evolution is strongly predictive of residue-residue contacts in the 3D structure of the protein. On this website, you can:. Submit contact prediction jobs for both monomers. Upload PDB models to see agreement to co-evolution data. Generate restraints to be used in Rosetta for modeling. We would also like to thank the developers of HHsuite.

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openseq.org

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OPENSEQ.org - GREMLIN Submission

http://www.openseq.org/sub.php?sort=name&order=DESC&uid=1398960977

Please contact us if you notice any strange outputs. Iter 4 -cov 75 -gap 75 -msa HHblits. Iter 4 -cov 75 -gap 75 -msa HHblits. Iter 4 -cov 75 -gap 75 -msa HHblits. Iter 4 -cov 75 -gap 75 -msa HHblits. Iter 4 -cov 75 -gap 75 -msa HHblits. Iter 4 -cov 75 -gap 75 -msa HHblits. Iter 4 -cov 75 -gap 75 -msa HHblits. Iter 4 -cov 75 -gap 75 -msa HHblits. Iter 8 -cov 75 -gap 75 -msa Jackhmmer. Iter 4 -cov 75 -gap 75 -msa HHblits. Iter 4 -cov 75 -gap 75 -msa HHblits. Iter 4 -cov 75 -gap 75 -msa Jackhmmer. Iter 4 -...

2

OPENSEQ.org - Pfam Coevolution Predictions

http://www.openseq.org/pfam.php

Please contact us if you notice any strange outputs. We've setup an online database that contain GREMLIN predictions for protein domains from the PFAM. Protein family database. The intent of this database is to give you an idea if GREMLIN might be useful for your gene (once you figure out. What protein family it might belong to.) If there are enough homologous sequences to perform the analysis, you can then either use these pre-computed predictions, or submit your sequence to our on-line server. HH delta...

3

OPENSEQ.org - GREMLIN Downloads

http://www.openseq.org/gremlin.php

Please contact us if you notice any strange outputs. Request for GREMLIN Source Code. Is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. Jan 08, 2014). Fixed a bug in sequence reweighting in the public version. Dec 24, 2012). This version that learns a Markov Random Field from an input alignment with parameters optimized for accuracy and speed of contact prediction. Used for Kamisetty et al. 2013 paper.

4

OPENSEQ.org - Pfam Coevolution Predictions

http://www.openseq.org/pfam.php?mode=full

Please contact us if you notice any strange outputs. List of ALL Protein Families. The intent of this list is to give you an idea if GREMLIN might be useful for your gene (once you figure out. What protein family it might belong to.). HH delta 0.5 means no known homolog (and/or we predict that GREMLIN is likely to provide more information on top of the closest known homolog). We find gremlin to be accurate when there are at least 5 Sequences/Length. Chal sti synt N. DNA pol viral N. Orn DAP Arg deC.

5

OPENSEQ.org - GREMLIN Submission

http://www.openseq.org/cplx_sub.php

Please contact us if you notice any strange outputs. CI 6 20 cI 9 10 tt. Delta;gene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015 06). CI 6 20 cI 9 20 tt. Delta;gene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015 06). CI 3 20 cI 4 20 tt. Delta;gene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015 06). CI 3 40 cI 9 40 tt. Delta;gene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015 06). Delta;gene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015 06). CI 3 20 cI 6 20 tt. Delta...

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opensequence.org

OpenSequence.org: Publications

http://www.opensequence.org/2009/09/literature-watch.html

The Freedom To Know. Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information. Sergey Ovchinnikov, Hetunandan Kamisetty, and David Baker. Assessing the utility of coevolution-based residue–residue contact predictions in a sequence-and structure-rich era. Hetunandan Kamisetty, Sergey Ovchinnikov, and David Baker. 110, no. 39 (2013): 15674-15679. Sergey Ovchinnikov, Susan E Masta. 31 (12 March 2012). Sergey Ovchinnikov, Mark Fishbein.

opensequence.org

OpenSequence.org: Welcome

http://www.opensequence.org/2009/09/news.html

The Freedom To Know. Welcome to OpenSequence.org. A little about me:. My name is Sergey Ovchinnikov. I majored in Micro/Molecular Biology and minored in Chemistry at Portland State University. I am currently a graduate student at University of Washington for the department of Molecular and Cellular Biology. My advisor is David Baker. Co-evolution (GREMLIN) based analysis can be found at OPENSEQ.org. A table, a chair, a bowl of fruit and a violin; what else does a man need to be happy?

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openseq.org

OPENSEQ.org

GREMLIN is a method to learn a statistical model of a protein family that captures both conservation and co-evolution patterns in the family. The strength of measured co-evolution is strongly predictive of residue-residue contacts in the 3D structure of the protein. On this website, you can:. Submit contact prediction jobs for both monomers. Upload PDB models to see agreement to co-evolution data. Generate restraints to be used in Rosetta for modeling. We would also like to thank the developers of HHsuite.

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opensequence.org

OpenSequence.org

The Freedom To Know. Welcome to OpenSequence.org. Welcome to OpenSequence.org. A little about me: My name is Sergey Ovchinnikov. I majored in Micro/Molecular Biology and minored in Chemistry at Portland State University. I am currently a graduate student at the University of Washington for the department of Molecular and Cellular Biology. My advisor is David Baker. Co-evolution (GREMLIN) based analysis can be found at OPENSEQ.org. Protein structure determination using metagenome sequence data.

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