---

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

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---

```{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 28/September/2023, 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>

- **JackHMMER**: <https://www.ebi.ac.uk/Tools/hmmer/search/jackhmmer>

- 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 services.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/Tools/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].\

# **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

- **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>

- **Openfold** [@ahdritz] Colab:

<https://colab.research.google.com/github/aqlaboratory/openfold/blob/main/notebooks/OpenFold.ipyn>

- **Unifold** [@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>

- **PymolFold**: A handy Pymol script that calls the ESM-Fold API

- <https://github.com/JinyuanSun/PymolFold>

- Web version: <http://103.79.77.89:8501/>

- **Zhang server**: <https://zhanggroup.org/services/>

- Multiple methods, including I-TASSER [@roy2010], C-I-TASSER [@zheng2021]

or I-TASSER-MTD, among others.

# **Model quality assessment**

- **QMEAN & QMEANDisCo** [@studer2020]: <https://swissmodel.expasy.org/qmean/>

- **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

- 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 qMultiple 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>