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---
title: "Modeling Resources"
date: "August 21, 2023"
date-modified: "`r Sys.Date()`"
format:
html:
page-layout: full
toc: true
toc-location: right
toc-depth: 2
number-sections: true
number-depth: 1
link-external-icon: true
link-external-newwindow: true
bibliography: references.bib
editor:
markdown:
wrap: 80
---
```{r echo=FALSE, output=FALSE}
library(webexercises)
```
::: callout-warning
### Disclaimer
This is not a comprehensive list of Protein Modeling resources. Rather, it
contains some of the references, methods, and online servers that I found useful
through the years.
Most useful links (IMHO) are highlighted in bold. Other (many) tools may be
useful for you, feel free to let me know and I'll update the list.
:::
::: callout-note
Links checked on 13/feb/2025, let me know if you find any broken link.
:::
# **Template search**
- **BLAST**: <https://blast.ncbi.nlm.nih.gov/Blast.cgi>
- **HHPRED**: <https://toolkit.tuebingen.mpg.de/tools/hhpred>
- **HHblits**: <https://toolkit.tuebingen.mpg.de/tools/hhblits>
- **HMMER**: <https://www.ebi.ac.uk/Tools/hmmer/>
- Ref. <https://nar.oxfordjournals.org/content/46/W1/W200>
# **Secondary structure and 1D features services**
- **Jpred4**: <http://www.compbio.dundee.ac.uk/jpred/>
- Secondary structure prediction
- Ref. <http://nar.oxfordjournals.org/content/early/2015/04/16/nar.gkv332>
- **PsiPred** : <http://bioinf.cs.ucl.ac.uk/psipred/>
- Secondary structure prediction
- MEMSAT-SVM (Membrane Helix Prediction)
- Ref: <https://academic.oup.com/nar/article/47/W1/W402/5480136>
- MULTICOM Toolbox:
<http://sysbio.rnet.missouri.edu/multicom_toolbox/web%20services.html>
- Pulls together protein structure and structural feature prediction
tools.
- ⚠️Server currently offline. Application available on GitHub:
<https://github.com/multicom-toolbox>
- SCRATCH: <http://scratch.proteomics.ics.uci.edu/>
- Metaserver with a wide range of 1D-3D prediction tools.
- SYMPRED: <http://www.ibi.vu.nl/programs/sympredwww/>
- Consensus secondary structure prediction metaserver
- MESSA: <http://prodata.swmed.edu/MESSA/MESSA.cgi>
- 1D features Metaserver
- Ref.<https://bmcbiol.biomedcentral.com/articles/10.1186/1741-7007-10-82>
- **DeepTMHMM**: <https://dtu.biolib.com/DeepTMHMM>
- Deep-learning 2022 version of the classic TMHMM predictor of
transmembrane helices
- Ref. <https://www.biorxiv.org/content/10.1101/2022.04.08.487609v1>
- Phobius: <https://www.ebi.ac.uk/jdispatcher/pfa/phobius>
- Prediction of transmembrane topology and signal peptides from the amino
acid sequence of a protein.
- TopCons: <http://topcons.cbr.su.se/>
- Consensus prediction of membrane protein topology and signal peptides
- Ref.
<https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkv485>
- PSORT: <https://psort.hgc.jp/>
- Several localization signals
- PRED-TMMB: <http://bioinformatics.biol.uoa.gr/PRED-TMBB/>
- Predicion of beta-barrel TMEs & topology (HMM-based)
- PROF-TMF: <https://open.predictprotein.org/>
- Predicion of beta-barrel TMEs (PredictProtein Suite)
- **NLStradamus**: <http://www.moseslab.csb.utoronto.ca/NLStradamus/>
- Prediction of NLS
- Sulfinator**:** <https://web.expasy.org/sulfinator/>
- Prediction of disulfide bonds
- **DTU Tech resources**: <https://services.healthtech.dtu.dk/>
- A collection of molecular biology tools, including a number of services
for 1D features prediction, such as DeepTMHMM [@hallgren] or NetSurfP
[@høie2022].
- **MobiDB**: <https://mobidb.org/>
- A database of protein disorder and mobility annotations [@piovesan2025].
# **Protein modeling**
- **SwissModel** [@waterhouse2018]: <https://swissmodel.expasy.org/>
- PsiPRED [@buchan2019]: <http://bioinf.cs.ucl.ac.uk/psipred/>
- Fold recognition server (among other tools)
- RaptorX [@wang2017]: <http://raptorx.uchicago.edu/ContactMap/>
- Distance-based Protein Folding Powered by Deep Learning.
- ⚠️Server currently offline
- Phyre2 [@kelley2015]:
<http://www.sbg.bio.ic.ac.uk/~phyre2/html/page.cgi?id=index>
- Fold recognition & fragment assembler
- **Robetta** server: <https://robetta.bakerlab.org/>
- Several methods, including RosettaCM [@song2013] and RoseTTAFOLD
[@baek2021a; @baeka]
- ModWeb [@pieper2014]**:** <https://modbase.compbio.ucsf.edu/modweb/>
- Webserver using MODELLER (free registration required)
- **ColabFold** [@mirdita2022]: <https://github.com/sokrypton/ColabFold>
- Several notebooks available
- DeepMind's AlphaFold colab:
<https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb>
- **AlphaFold Server** [@abramson2024]: <https://alphafoldserver.com/>
- Requires registration to build up to 20 models per day, including
proteins involving more than one chain, nucleic acids or some small
molecules from a (small) list.
- **Chai-1 Server** [@discovery]: <https://lab.chaidiscovery.com/>
- Requires registration to build up to 25 models per day, including
proteins involving more than one chain, nucleic acids some small
molecules in
[SMILES](https://en.wikipedia.org/wiki/Simplified_Molecular_Input_Line_Entry_System)
format.
- **OpenFold** [@ahdritz] Colab:
<https://colab.research.google.com/github/aqlaboratory/openfold/blob/main/notebooks/OpenFold.ipynb>
- **Uni-fold** [@li] Colab:
<https://colab.research.google.com/github/dptech-corp/Uni-Fold/blob/main/notebooks/unifold.ipynb>
- **ESM Metagenomic Atlas** (DDBB & tools, @lin2023):
<https://esmatlas.com/about>
- **Zhang server**: <https://zhanggroup.org/services/>
- Multiple methods, including I-TASSER [@roy2010], C-I-TASSER [@zheng2021]
or I-TASSER-MTD, among others.
- PymolFold: A handy Pymol script that calls the ESM-Fold API
- <https://github.com/JinyuanSun/PymolFold>
- **PyMOLFold** [@ford] (yes, duplicated name 🤷🏻♂️) is a another Pymol extension
that allow modeling protein complexes using ESM3, Chai-1 and Boltz-1
installed in different Conda environments. It can work with CPU or GPU, but
seems slow if you have only CPU.
- <https://github.com/colbyford/PyMOLfold>
- **Alphafold2import**: <https://github.com/APAJanssen/Alphafold2import>
- PyMOL plugin to import structures from Alphafold2 database
- **Pymol-color-alphafold**:
<https://github.com/cbalbin-bio/pymol-color-alphafold>
- This is a Pymol extension to color structures by the AlphaFold pLDDT
color-code. Use it only with AF or similar models that contain the pLDDT
in the B-factor column of the PDB file.
- **Pymol plugins repo**:
<https://wiki.pymol.org/index.php/Category:Pymol-script-repo>
# **Model quality assessment**
- **QMEAN & QMEANDisCo** [@studer2020; @waterhouse2024]:
<https://swissmodel.expasy.org/assess>
- **Modfold** [@mcguffin2021]**:** <https://www.reading.ac.uk/bioinf/ModFOLD/>
- **VoroMQA** [@olechnovic2019]**:
<http://bioinformatics.ibt.lt/wtsam/voromqa>**
- **DeepUMQA** [@guo2022]: <http://zhanglab-bioinf.com/DeepUMQA/>
# **Other resources**
- **DALI** [@holm2022]: <http://ekhidna2.biocenter.helsinki.fi/dali/>
- **FoldSeek** [@vankempen2023]: <https://search.foldseek.com/search>
- Fast search for structural similarities (server & API)
- CryoNet [@guo2024]: <https://cryonet.ai/bseek/>
- Fast search for structural similarities
- FatCat [@li2020]: <http://fatcat.godziklab.org/fatcat/fatcat_pair.html>
- Structural alignment tool.
- LGA: <http://proteinmodel.org/AS2TS/LGA/lga.html>
- LGA program is being developed for structure comparative analysis of two
selected 3D protein structures or fragments of 3D protein structures
- Ref.
<https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkg571>
- Galaxy Refine: <http://galaxy.seoklab.org/cgi-bin/submit.cgi?type=REFINE>
- A server for automatically refining protein model structures.
- Ref. <http://www.ncbi.nlm.nih.gov/pubmed/23737448>
- Galaxy Refine2:
[[galaxy.seoklab.org/cgi-bin/submit.cgi?type=REFINE2]{.underline}](http://galaxy.seoklab.org/cgi-bin/submit.cgi?type=REFINE2)
- \<300 aa
- Ref:<https://academic.oup.com/nar/article/47/W1/W451/5475172>
- HOMCOS: <http://homcos.pdbj.org/>
- Modeling of 3D Structures of Complexes
- Ref.
<http://link.springer.com/article/10.1007/s10969-016-9208-y?wt_mc=Internal.Event.1.SEM.ArticleAuthorOnlineFirst>
- pyDockWEB: <https://life.bsc.es/pid/pydockweb>
- Prediction of protein-protein interactions (hetero-oligomers modeling)
- Hex: <http://hexserver.loria.fr/>
- Prediction of protein-protein interactions (homo- & hetero-oligomers
modeling)
- Ref. <https://onlinelibrary.wiley.com/doi/full/10.1002/prot.24433>
- DaReUs-Loop**:**
<https://bioserv.rpbs.univ-paris-diderot.fr/services/DaReUS-Loop/>
- Modeling loops
- Ref. <https://www.nature.com/articles/s41598-018-32079-w>
- GalaxyLoop: <http://galaxy.seoklab.org/cgi-bin/submit.cgi?type=LOOP>
- Loops refining
- Ref.
<https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0113811>
- Expasy proteomics tools: <https://www.expasy.org/proteomics>
- List of Multiple links and resources
- Protein modeling links \@Sali Lab:
<https://salilab.org/bioinformatics_resources.html>
- Homology modeling \@Proteopedia:
- <https://proteopedia.org/wiki/index.php/Homology_model>
- <https://proteopedia.org/wiki/index.php/User:Wayne_Decatur/Homology_Modeling>
- List of protein structure prediction software \@Wikipedia:
<https://en.wikipedia.org/wiki/List_of_protein_structure_prediction_software>