References

If you are using models from the SWISS-MODEL Server or Repository, please cite the corresponding articles:

SWISS-MODEL Workspace / GMQE
Waterhouse A, Bertoni M, Bienert S, Studer G, Tauriello G, Gumienny R, Heer FT, de Beer TAP, Rempfer C, Bordoli L, Lepore R, Schwede T
SWISS-MODEL: homology modelling of protein structures and complexes.
Nucleic Acids Res 46, W296-W303. (2018) 29788355 10.1093/nar/gky427
SWISS-MODEL Repository
Bienert S, Waterhouse A, de Beer TAP, Tauriello G, Studer G, Bordoli L, Schwede T
The SWISS-MODEL Repository - new features and functionality.
Nucleic Acids Res 45, D313-D319. (2017) 27899672 10.1093/nar/gkw1132
Structure Assessment
Waterhouse AM, Studer G, Robin X, Bienert S, Tauriello G, Schwede T
The structure assessment web server: for proteins, complexes and more.
Nucleic Acids Res, gkae270 Epub ahead of print. (2024) 38634802 10.1093/nar/gkae270
Swiss-PdbViewer/ DeepView project mode
Guex N, Peitsch MC, Schwede T
Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: A historical perspective.
Electrophoresis 30, S162-S173. (2009) 19517507 10.1002/elps.200900140
ProMod3
Studer G, Tauriello G, Bienert S, Biasini M, Johner N, Schwede T
ProMod3 - A versatile homology modelling toolbox.
PLOS Comp Biol 17(1), e1008667. (2021) 33507980 10.1371/journal.pcbi.1008667
QMEANDisCo
Studer G, Rempfer C, Waterhouse AM, Gumienny R, Haas J, Schwede T
QMEANDisCo - distance constraints applied on model quality estimation.
Bioinformatics 36, 1765-1771. (2020) 31697312 10.1093/bioinformatics/btz828
QMEANBrane
Studer G, Biasini M, Schwede T
Assessing the local structural quality of transmembrane protein models using statistical potentials (QMEANBrane).
Bioinformatics 30, i505–i511. (2014) 25161240 10.1093/bioinformatics/btu457
QMEAN
Benkert P, Biasini M, Schwede T
Toward the estimation of the absolute quality of individual protein structure models.
Bioinformatics 27, 343-350. (2011) 21134891 10.1093/bioinformatics/btq662
Quaternary Structure Prediction/ QSQE
Bertoni M, Kiefer F, Biasini M, Bordoli L, Schwede T
Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology.
Scientific Reports 7. (2017) 28874689 10.1038/s41598-017-09654-8
lDDT
Mariani V, Biasini M, Barbato A, Schwede T
lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests.
Bioinformatics 29, 2722-2728. (2013) 23986568 10.1093/bioinformatics/btt473
Click for a chronological assembly of SWISS-MODEL publications.
- Robin X, Waterhouse AM, Bienert S, Studer G, Alexander LT, Tauriello G, Schwede T, Pereira J
  The SWISS-MODEL Repository of 3D Protein Structures and Models.
  Open Access Databases and Datasets for Drug Discovery, 175-199. (2023) 10.1002/9783527830497.ch6
- Studer G, Tauriello G, Bienert S, Waterhouse AM, Bertoni M, Bordoli L, Schwede T, Lepore R
  Modeling of Protein Tertiary and Quaternary Structures Based on Evolutionary Information.
  Methods Mol Biol 1851, 301-316. (2019) 30298405 10.1007/978-1-4939-8736-8_17
- Biasini M, Bienert S, Waterhouse A, Arnold K, Studer G, Schmidt T, Kiefer F, Cassarino TG, Bertoni M, Bordoli L, Schwede T
  SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information.
  Nucleic Acids Res 42, W252-W258. (2014) 24782522 10.1093/nar/gku340
- Mariani V, Biasini M, Barbato A, Schwede T
  lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests.
  Bioinformatics 29, 2722-2728. (2013) 23986568 10.1093/bioinformatics/btt473
- Bordoli L, Schwede T
  Automated protein structure modeling with SWISS-MODEL Workspace and the Protein Model Portal.
  Methods Mol Biol 857, 107-136. (2012) 22323219 10.1007/978-1-61779-588-6_5
- Bordoli L, Kiefer F, Arnold K, Benkert P, Battey J, Schwede T
  Protein structure homology modeling using SWISS-MODEL workspace.
  Nat Protoc 4, 1–13. (2009) 19131951 10.1038/nprot.2008.197
- Kiefer F, Arnold K, Kuenzli M, Bordoli L, Schwede T
  The SWISS-MODEL Repository and associated resources.
  Nucleic Acids Res 37, D387–D392. (2009) 18931379 10.1093/nar/gkn750
- Benkert P, Künzli M, Schwede T
  QMEAN server for protein model quality estimation.
  Nucleic Acids Res 37, W510-W514. (2009) 19429685 10.1093/nar/gkp322
- Benkert P, Schwede T, Tosatto SCE
  QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density information.
  BMC Struct Biol 9, 35. (2009) 19457232 10.1186/1472-6807-9-35
- Arnold K, Bordoli L, Kopp J, Schwede T
  The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling.
  Bioinformatics 22, 95-201. (2006) 16301204 10.1093/bioinformatics/bti770
- Kopp J, Schwede T
  The SWISS-MODEL Repository: new features and functionalities.
  Nucleic Acids Res 34, D315–D318. (2006) 16381875 10.1093/nar/gkj056
- Kopp J, Schwede T
  The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models.
  Nucleic Acids Res 32, D230–D234. (2004) 14681401 10.1093/nar/gkh008
- Schwede T, Kopp J, Guex N, Peitsch MC
  SWISS-MODEL: an automated protein homology-modeling server.
  Nucleic Acids Res 31, 3381-3385. (2003) 12824332 10.1093/nar/gkg520
- Guex N, Diemand A, Peitsch MC
  Protein modelling for all.
  Trends Biochem Sci 24, 364 - 367. (1999) 10470037 10.1016/S0968-0004(99)01427-9
- Guex N, Peitsch MC
  SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling.
  Electrophoresis 18, 2714-2723. (1997) 9504803 10.1002/elps.1150181505
- Peitsch MC
  ProMod and Swiss-Model: Internet-based tools for automated comparative protein modelling.
  Biochem Soc Trans 24, 274-279. (1996) 8674685 10.1042/bst0240274
- Peitsch MC, Herzyk P, Wells TN, Hubbard RE
  Automated modelling of the transmembrane region of G-protein coupled receptor by Swiss-model.
  Recept Channels 4, 161-4. (1996) 9014239
- Peitsch MC, Tschopp J
  Comparative molecular modelling of the Fas-ligand and other members of the TNF family.
  Mol Immunol 32, 761-772. (1995) 7544870 10.1016/0161-5890(95)00016-8
- Peitsch MC
  Protein Modeling by E-mail.
  Biotechnology (N.Y.) 13, 658–660. (1995) 10.1038/nbt0795-658
- Peitsch MC, Jongeneel CV
  A 3-D model for the CD40 ligand predicts that it is a compact trimer similar to the tumor necrosis factors.
  Int Immunol 5, 233-238. (1993) 8095800 10.1093/intimm/5.2.233

SWISS-MODEL would not be possible without the following resources and tools

AlphaFold Protein Structure Database
Varadi M, Anyango S, Deshpande M, Nair S, Natassia C, Yordanova G, Yuan D, Stroe O, Wood G, Laydon A, Žídek A, Green T, Tunyasuvunakool K, Petersen S, Jumper J, Clancy E, Green R, Vora A, Lutfi M, Figurnov M, Cowie A, Hobbs N, Kohli P, Kleywegt G, Birney E, Hassabis D, Velankar S
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models.
Nucleic Acids Res., 50, D439–D444. (2022) 34791371 10.1093/nar/gkab1061
BLAST
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL
BLAST+: architecture and applications.
BMC Bioinformatics, 10, 421-430. (2009) 20003500 10.1186/1471-2105-10-421
BLOSUM62
Henikoff S, Henikoff JG
Amino acid substitution matrices from protein blocks.
Proc Natl Acad Sci USA, 89(22): 10915-10919. (1992) 31704957 10.1038/s41598-019-52532-8
CAMEO - Continuous Automated Model EvaluatiOn
Haas J, Barbato A, Behringer D, Studer G, Roth S, Bertoni M, Mostaguir K, Gumienny R, Schwede T
Continuous Automated Model EvaluatiOn (CAMEO) complementing the critical assessment of structure prediction in CASP12.
Proteins. (2017) 29178137 10.1002/prot.25431
CD-HIT
Li W, L. Jaroszewski, Godzik A
Sequence clustering strategies improve remote homology recognitions while reducing search times.
Protein Eng 15(8): 643-649. (2002) 12364578 10.1093/protein/15.8.643
ClustalW2
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG
Clustal W and Clustal X version 2.0.
Bioinformatics, 23, 2947-2948. (2007) 17846036 10.1093/bioinformatics/btm404
CHARMM22/CMAP
Mackerell AD Jr, Feig M, Brooks CL 3rd
Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations.
J Comput Chem 25(11):1400-15. (2004) 15185334 10.1002/jcc.20065
DSSP
Kabsch W, Sander C
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.
Biopolymers 22: 2577-2637. (1983) 6667333 10.1002/bip.360221211
Fast Searching of Large Sequence Databases
Goddard T
Fast Searching of Large Sequence Databases.
https://www.rbvi.ucsf.edu/chimerax/data/kmer-aug2022/kmer_search.html
Graphviz
Ellson J, Gansner E, Koutsofios L, North SC, Woodhull G
Graphviz - Open Source Graph Drawing Tools.
Mutzel P., Jünger M., Leipert S (eds) Graph Drawing GD 2001 Lecture Notes in Computer Science, vol 2265 Springer, Berlin, Heidelberg. (2002) 10.1007/3-540-45848-4_57
GISAID
Elbe S, Buckland-Merrett G
Data, disease and diplomacy: GISAID’s innovative contribution to global health.
Global Challenges 1: 33-46. (2017) 31565258 10.1002/gch2.1018
Gromos
van Gunsteren WF
Biomolecular Simulations: The GROMOS96 Manual and User Guide Zürich, VdF Hochschulverlag ETHZ.
HHblits
Steinegger M, Meier M, Mirdita M, Vöhringer H, Haunsberger SJ, Söding J
HH-suite3 for fast remote homology detection and deep protein annotation.
BMC Bioinformatics 20, 473. (2019) 31521110 10.1186/s12859-019-3019-7
HighCharts
JavaScript library https://www.highcharts.com.
InterPro
Jones P, Binns D, Chang H, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, Pesseat S, Quinn AF, Sangrador-Vegas A, Scheremetjew M, Yong S, Lopez R, Hunter S
InterProScan 5: genome-scale protein function classification.
Bioinformatics, Jan 2014. (2014) 24451626 10.1093/bioinformatics/btu031
jQuery
JavaScript Library.
https://jquery.com/
Matplotlib
Hunter JD
Matplotlib: A 2D graphics environment.
Comput Sci Eng 9, 90-95. (2007) 10.1109/MCSE.2007.55
Membrane Prediction
Lomize AL, Pogozheva ID, Lomize MA, Mosberg HI
Positioning of proteins in membranes: A computational approach.
Protein Sci. (2006) 16731967 10.1110/ps.062126106
MolProbity
Chenn VB, Arendall WB, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC
All-atom structure validation for macromolecular crystallography.
Acta Cryst D66, 16-21. (2010) 20057044 10.1107/S0907444909042073
Molscript:
Kraulis PJ
MOLSCRIPT: A Program to Produce Both Detailed and Schematic Plots of Protein Structures,.
Journal of Applied Crystallography24, 946-950. (1991) 10.1107/S0021889891004399
NGL
Rose AS, Bradley AR, Valasatava Y, Duarte JM, Prlić A, Rose PW
NGL viewer: web-based molecular graphics for large complexes Bioinformatics: bty419, 2018 AS Rose and PW Hildebrand NGL Viewer: a web application for molecular visualization.
Nucl Acids Res (1 July 2015) 43 (W1): W576-W579 first published online April 29, 2015. (2015) 25925569 10.1093/nar/gkv402
OpenMM
Eastman P, Swails J, Chodera JD, McGibbon RT, Zhao Y, Beauchamp KA, Wang LP, Simmonett AC, Harrigan MP, Stern CD, Wiewiora RP, Brooks BR, Pande VS
OpenMM 7: Rapid Development of High Performance Algorithms for Molecular Dynamics.
PLoS Comput Biol 2017. (2017) 28746339 10.1371/journal.pcbi.1005659
OpenStructure (OST)
Biasini M, Schmidt T, Bienert S, Mariani V, Studer G, Haas J, Johner N, Schenk AD, Philippsen A, Schwede T
OpenStructure: an integrated software framework for computational structural biology.
Acta Cryst 2013. (2013) 23633579 10.1107/S0907444913007051
PDB
Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, Burkhardt K, Feng Z, Gilliland G.L. Iype, L. Jain, S. Fagan P, Marvin J, Padilla D, Ravichandran V, Schneider B, Thanki N, Weissig H, Westbrook JD, Zardecki C
The Protein Data Bank.
Nucleic Acids Res, 28, 235-242. (2000) 12037327 10.1107/s0907444902003451

Berman H, Henrick K, Nakamura H, Markley JL

The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data.

Nucleic Acids Res, 35, D301-303. (2007) PubMed logo

17142228

10.1093/nar/gkl971

PISCES
Wang G, Dunbrack RL Jr
PISCES: A protein sequence culling server.
Bioinformatics 19:1589–1591.(2016). (2003) 12912846 10.1093/bioinformatics/btg224
PFAM
Finn RD, Coggill P, Eberhardt RY, Edd SR, Mistry J, Mitchell AL, Potter SC, Punta M, Qureshi M, Sangrador-Vegas A, Salazar GA, Tate J, Bateman A
The Pfam protein families database: towards a more sustainable future.
Nucleic Acids Research (2016) Database Issue 44:D279-D285. (2016) 26673716 10.1093/nar/gkv1344
PLIP
Adasme MF, Linnemann KL, Bolz SN, Kaiser F, Salentin S, Haupt VJ, Schroeder M
PLIP 2021: expanding the scope of the protein–ligand interaction profiler to DNA and RNA.
Nucleic Acids Research 49 (Web Server issue):W530-W534 doi:10.1093/nar/gkab294. (2021) 33950214 10.1093/nar/gkab294
PsiPred
Jones DT
Protein secondary structure prediction based on position-specific scoring matrices.
J Mol Biol 292(2): 195-202. (1999) 10493868 10.1006/jmbi.1999.3091
PV
Biasini M
PV - WebGL-based Protein Viewer.
10.5281/zenodo.12620
InterPro
Mulder NJ, Apweiler R, Attwood T K, Bairoch A, Bateman A, Binns D, Bradley P, Bork P, Bucher P, Cerutti L, Copley R, Courcelle E, Das U, Durbin R, Fleischmann W, Gough J, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McDowall J, Mitchell A, Nikolskaya A N, Orchard S, Pagni M, Ponting C P, Quevillon E, Selengut J, Sigrist C J, Silventoinen V, Studholme D J, Vaughan R, Wu CH
InterPro, progress and status in 2005.
Nucleic Acids Res 33 Database Issue: D201-205. (2005) 15608177 10.1093/nar/gki106
Raphaël JS
JavaScript Library.
https://jquery.com/
Raster3D
Merritt EA, Bacon DJ
Raster3D Photorealistic Molecular Graphics.
Methods in Enzymology 1997, 277 505-524. (1997) 18488322 10.1016/s0076-6879(97)77028-9
SCRWL4
Krivov GG, Shapovalov MV, Dunbrack RL Jr
Improved prediction of protein side-chain conformations with SCWRL4.
Proteins 2009. (2009) 19603484 10.1002/prot.22488
SIFTS
Velankar S, Dana JM, Jacobsen J, van Ginkel G, Gane PJ, Luo J, Oldfield TJ, O'Donovan C, Martin MJ, Kleywegt GJ
SIFTS: Structure Integration with Function, Taxonomy and Sequences resource.
Nucleic acids research, 41, D483-489. (2013) 23203869 10.1093/nar/gks1258
SSpro / ACCpro
Cheng J, Randall AZ, Sweredoski MJ, Baldi P
SCRATCH: a Protein Structure and Structural Feature Prediction Server.
Nucleic Acids Research, vol 33 (web server issue), w72-76. (2005) 15980571 10.1093/nar/gki396
STRING
Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P, Jensen LJ, von Mering C
STRING v10: protein-protein interaction networks, integrated over the tree of life.
Nucleic Acids Res, 43, D447-52. (2015) 25352553 10.1093/nar/gku1003
SwissDock
Grosdidier A, Zoete V, Michielin O
SwissDock, a protein-small molecule docking web service based on EADock DSS.
Nucleic Acids Res, 39, W270-7. (2011) 21624888 10.1093/nar/gkr366

Grosdidier A, Zoete V, Michielin O

Fast docking using the CHARMM force field with EADock DSS.

J Comput Chem 32(10), 2149-59. (2011) PubMed logo

21541955

10.1002/jcc.21797

TreePack
Xu J, Jiao F, Berger B
A tree-decomposition approach to protein structure prediction.
Proc IEEE Comput Syst Bioinform Conf, 247-56. (2005) 16447982 10.1109/csb.2005.9
Uniclust
Mirdita M, von den Driesch L, Galiez C, Martin MJ, Söding J, Steinegger M
Uniclust databases of clustered and deeply annotated protein sequences and alignments.
Nucleic Acids Res, 45, D170–D176. (2016) 27899574 10.1093/nar/gkw1081
UniProtKB
UniProt: the universal protein knowledgebase.
Nucleic Acids Res, 45, D158-D169. (2017) 27899622 10.1093/nar/gkw1099