links.qmd

---
title: "Modeling Resources"
author: "Modesto Redrejo Rodríguez"
date: "`r Sys.Date()`"
format:
  html:
    theme: morph
    toc: true
    number-sections: false
---

::: callout-note
### 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.
:::

Links accessed on 21/September/2022

### **1. Template search**

-   **BLAST**: <https://blast.ncbi.nlm.nih.gov/Blast.cgi>

-   **HHPRED**: <https://toolkit.tuebingen.mpg.de/tools/hhpred>

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

    -   Ref. <https://nar.oxfordjournals.org/content/46/W1/W200>

### **2. 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

-   Genesilico: <http://genesilico.pl/>

    -   Secondary structure prediction metaserver (currently out of service!)

-   **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, includin a number of services for 1D features prediction\

### **3. Protein modeling**

-   **SwissModel**: <https://swissmodel.expasy.org/>

    -   Ref: <https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gky427>

-   **Robetta** server: <https://robetta.bakerlab.org/>

    -   Several methods

-   **ModWeb:** <https://modbase.compbio.ucsf.edu/modweb/>

    -   Webserver using MODELLER (free registration required)

    -   Ref. <https://pubmed.ncbi.nlm.nih.gov/24271400/>

-   **ColabFold**: <https://github.com/sokrypton/ColabFold>

    -   Several notebooks available

    -   Ref. <https://www.nature.com/articles/s41592-022-01488-1>

-   CPHmodels: <https://services.healthtech.dtu.dk/service.php?CPHmodels-3.2>

    -   Ref: <https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkq535>

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

    -   Multiple methods, including I-TASSER, C-I-TASSER or I-TASSER-MTD

    -   See references within.

-   PsiPRED: <http://bioinf.cs.ucl.ac.uk/psipred/>

    -   Fold recognition server (among other tools)

    -   Ref: <https://academic.oup.com/nar/article/47/W1/W402/5480136>

-   Multicom: <http://sysbio.rnet.missouri.edu/multicom_cluster/>

    -   Ref.<https://bmcstructbiol.biomedcentral.com/articles/10.1186/1472-6807-13-2>

-   **RaptorX**: <http://raptorx.uchicago.edu/ContactMap/>

    -   Distance-based Protein Folding Powered by Deep Learning

    -   Ref. <https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005324>

-   **Phyre2**: <http://www.sbg.bio.ic.ac.uk/~phyre2/html/page.cgi?id=index>

    -   Ref. <http://www.nature.com/nprot/journal/v10/n6/ris/nprot.2015.053.ris>

    -   Fold recognition & fragment assembler\

### **4. Model quality assessment**

-   **QMEAN**: <https://swissmodel.expasy.org/qmean/>

    -   Includes the new version QMEANDisCo

    -   Ref. <https://doi.org/10.1093/bioinformatics/btz828>

-   **Modfold: <https://www.reading.ac.uk/bioinf/ModFOLD/ModFOLD6_form.html>**

    -   Ref: <https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkx332>

-   **VoroMQA: <http://bioinformatics.ibt.lt/wtsam/voromqa>**

    -   Ref: <https://onlinelibrary.wiley.com/doi/full/10.1002/prot.25278>

-   Saves: <https://servicesn.mbi.ucla.edu/SAVES/>

    -   Quality assessment in several "classic" servers

-   SIFT: <http://sift.cchmc.org/>

    -   **S**equence **I**ndependent (as well as dependent) **F**iltering **T**ools for efficient and accurate protein model quality assessment

    -   Ref. <https://www.tandfonline.com/doi/abs/10.1080/00268970410001728636?journalCode=tmph20>

### **5. Other resources**

-   **DALI**: <http://ekhidna2.biocenter.helsinki.fi/dali/>

    -   Web service for comparing protein structures in 3D

    -   Ref:<https://onlinelibrary.wiley.com/doi/full/10.1002/pro.3749>

-   **FoldSeek**: <https://search.foldseek.com/search>

    -   Find structural homologs

    -   Ref. <https://www.biorxiv.org/content/10.1101/2022.02.07.479398v4>

-   FatCat**:** <http://fatcat.godziklab.org/fatcat/fatcat_pair.html>

    -   Pairwise structural alignment of PDB entries or .pdb files.

    -   Ref. <https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkaa443>

-   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]{.ul}](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>