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, F.T., de Beer, T.A.P., Rempfer, C., Bordoli, L., Lepore, R., Schwede, T.
SWISS-MODEL: homology modelling of protein structures and complexes.
Nucleic Acids Res. 46, W296-W303 (2018).
SWISS-MODEL Repository
Bienert, S., Waterhouse, A., de Beer, T.A.P., Tauriello, G., Studer, G.,
Bordoli, L., Schwede, T. The SWISS-MODEL Repository - new features
and functionality. Nucleic Acids Res. 45, D313-D319 (2017).
Swiss-PdbViewer/ DeepView project mode
Guex, N., Peitsch, M.C., Schwede, T. Automated comparative protein
structure modeling with SWISS-MODEL and Swiss-PdbViewer: A historical
perspective. Electrophoresis 30, S162-S173 (2009).
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).
QMEANDisCo
Studer, G., Rempfer, C., Waterhouse, A.M., Gumienny, R., Haas, J.,
Schwede, T. QMEANDisCo - distance constraints applied on model quality
estimation. Bioinformatics 36, 1765-1771 (2020).
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).
QMEAN
Benkert, P., Biasini, M., Schwede, T. Toward the estimation
of the absolute quality of individual protein structure
models. Bioinformatics 27, 343-350 (2011).
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).
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).
Studer, G., Tauriello, G., Bienert, S., Waterhouse, A.M.,
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).
Biasini, M., Bienert, S., Waterhouse, A., Arnold, K.,
Studer, G., Schmidt, T., Kiefer, F., Cassarino, T.G.,
Bertoni, M., Bordoli, L., Schwede, T. SWISS-MODEL: modelling
protein tertiary and quaternary structure using evolutionary
information. Nucleic Acids Res. 42, W252-W258 (2014).
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).
Bordoli, L., Schwede T. Automated protein structure
modeling with SWISS-MODEL Workspace and the Protein Model
Portal. Methods Mol. Biol. 857, 107-136 (2012).
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).
Kiefer, F., Arnold, K., Kuenzli, M., Bordoli, L.,
Schwede, T. The SWISS-MODEL Repository and associated
resources. Nucleic Acids Res. 37, D387–D392 (2009).
Benkert, P., Künzli, M., Schwede, T. QMEAN server for
protein model quality estimation. Nucleic Acids Res. 37,
W510-W514 (2009).
Benkert, P., Schwede, T., Tosatto, S.C.E. QMEANclust:
estimation of protein model quality by combining a
composite scoring function with structural density
information. BMC Struct. Biol. 9, 35 (2009).
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).
Kopp, J., Schwede, T. The SWISS-MODEL Repository: new
features and functionalities. Nucleic Acids Res. 34,
D315–D318 (2006).
Kopp, J., Schwede, T. The SWISS-MODEL Repository of
annotated three-dimensional protein structure homology
models. Nucleic Acids Res. 32, D230–D234 (2004).
Schwede, T., Kopp, J., Guex, N., Peitsch, M.C. SWISS-MODEL:
an automated protein homology-modeling server. Nucleic
Acids Res. 31, 3381-3385 (2003).
Guex, N., Diemand, A., Peitsch, M.C. Protein modelling for
all. Trends Biochem. Sci. 24, 364 - 367 (1999).
Guex, N., Peitsch, M.C. SWISS-MODEL and the Swiss-PdbViewer:
an environment for comparative protein modeling.
Electrophoresis 18, 2714-2723 (1997).
Peitsch, M.C. ProMod and Swiss-Model: Internet-based tools
for automated comparative protein modelling. Biochem. Soc.
Trans. 24, 274-279 (1996)
Peitsch, M.C., Herzyk, P., Wells, T.N., Hubbard, R.E.
Automated modelling of the transmembrane region of
G-protein coupled receptor by Swiss-model. Recept. Channels
4, 161-4 (1996).
Peitsch, M.C., Tschopp, J. Comparative molecular modelling
of the Fas-ligand and other members of the TNF family. Mol.
Immunol. 32, 761-772 (1995).
Peitsch, M.C. Protein Modeling by E-mail. Biotechnology
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Peitsch, M.C., Jongeneel, C.V. 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).
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. (2022) AlphaFold
Protein Structure Database: massively expanding the structural coverage of
protein-sequence space with high-accuracy models. Nucleic Acids Res., 50,
D439–D444.
BLAST
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K.
and Madden, T.L. (2009) BLAST+: architecture and applications. BMC
Bioinformatics, 10, 421-430.
BLOSUM62
Henikoff S. and Henikoff J. G. (1992) Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA, 89(22): 10915-10919.
CAMEO - Continuous Automated Model EvaluatiOn
Haas, J., Barbato, A., Behringer, D., Studer, G., Roth, S.,
Bertoni, M., Mostaguir, K., Gumienny, R., Schwede, T. (2017)
Continuous Automated Model EvaluatiOn (CAMEO) complementing the
critical assessment of structure prediction in CASP12. Proteins.
CD-HIT Li, W., L., Jaroszewski, Godzik, A. (2002). "Sequence
clustering strategies improve remote homology recognitions while reducing
search times." Protein Eng 15(8): 643-649.
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.
(2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.
CHARMM22/CMAP Mackerell AD Jr, Feig M., Brooks CL 3rd. (2004). "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.
DSSP Kabsch, W. and C. Sander (1983). "Dictionary of
protein secondary structure: pattern recognition of hydrogen-bonded and
geometrical features." Biopolymers 22: 2577-2637.
Graphviz Ellson J., Gansner E., Koutsofios L., North S.C., Woodhull G.
(2002) Graphviz— Open Source Graph Drawing Tools. In: Mutzel P., Jünger M.,
Leipert S. (eds) Graph Drawing. GD 2001. Lecture Notes in Computer Science,
vol 2265. Springer, Berlin, Heidelberg
GISAID Elbe S., and Buckland-Merrett G. (2017) "Data, disease and diplomacy:
GISAID’s innovative contribution to global health." Global Challenges 1: 33-46
Gromos van Gunsteren, W. F. (1996).
Biomolecular Simulations: The GROMOS96 Manual and User Guide. Zürich,
VdF Hochschulverlag ETHZ.
HHblits Steinegger, M., Meier, M., Mirdita, M., Vöhringer, H., Haunsberger, S. J., Söding, J. (2019). "HH-suite3 for fast remote homology detection and deep protein annotation.", BMC Bioinformatics 20, 473.
InterPro
Jones P., Binns D., Chang H., Fraser M, Li W, McAnulla C, McWilliam H, Maslen J,
Mitchell A., Nuka G., Pesseat S., Quinn A.F., Sangrador-Vegas A., Scheremetjew M.,
Yong S., Lopez R., and Hunter S. (2014). InterProScan 5: genome-scale protein
function classification. Bioinformatics, Jan 2014.
jQuery JavaScript Library https://jquery.com/
Matplotlib
Hunter, J. D. (2007). "Matplotlib: A 2D graphics environment", Comput Sci Eng 9, 90-95.
Membrane Prediction
Lomize, A.L., Pogozheva I.D., Lomize M.A., Mosberg H.I. (2006). Positioning of proteins in membranes: A computational approach. Protein Sci.
Molscript:
Per J. Kraulis (1991) MOLSCRIPT: A Program to Produce Both Detailed
and Schematic Plots of Protein Structures, Journal of Applied Crystallography24, 946-950.
NGL
AS Rose, AR Bradley, Y Valasatava, JM Duarte, A Prlić and PW Rose. Web-based molecular graphics for large complexes. ACM Proceedings of the 21st International Conference on Web3D Technology (Web3D '16): 185-186, 2016.
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.
OpenMM Eastman P., Swails J., Chodera J. D., McGibbon R. T., Zhao Y., Beauchamp K. A.,
Wang L. P., Simmonett A. C., Harrigan M. P., Stern C. D., Wiewiora R. P., Brooks B. R.,
Pande V. S. (2017). "OpenMM 7: Rapid Development of High Performance Algorithms
for Molecular Dynamics." PLoS Comput. Biol. 2017.
OpenStructure (OST) Biasini M., Schmidt T., Bienert S., Mariani V., Studer G., Haas J., Johner N., Schenk A.D., Philippsen A. and Schwede T. (2013) "OpenStructure: an integrated software framework for computational structural biology." Acta Cryst 2013.
PDB Berman, H., Westbrook J., Feng Z., Gilliland G., Bhat T. N., Weissig I., Shindyalov I., Bourne P. E. (2000) "The Proten Data Bank". Nucleic Acids Res, 28, 235-242.
Berman, H., Henrick, K., Nakamura, H. and Markley, J.L. (2007) The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res, 35, D301-303.
PISCES
Wang G, Dunbrack RL Jr.
(2003) PISCES: A protein sequence culling server. Bioinformatics 19:1589–1591.(2016)
PFAM
R.D. Finn, P. Coggill, R.Y. Eberhardt, S.R. Eddy, J. Mistry, A.L. Mitchell,
S.C. Potter, M. Punta, M. Qureshi, A. Sangrador-Vegas, G.A. Salazar,
J. Tate, A. Bateman (2016) The Pfam protein families database: towards a
more sustainable future. Nucleic Acids Research (2016) Database Issue 44:D279-D285
PLIP
M.F. Adasme, K.L. Linnemann, S.N. Bolz, F. Kaiser, S. Salentin, V.J. Haupt, M. Schroeder (2021)
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.
PsiPred Jones, D. T. (1999). "Protein secondary
structure prediction based on position-specific scoring matrices."
J Mol Biol 292(2): 195-202.
PV Biasini, M. (2014). "PV - WebGL-based Protein Viewer."
InterPro Mulder, N. J., 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, C. H. (2005). "InterPro,
progress and status in 2005." Nucleic Acids Res 33 Database Issue:
D201-205.
Raster3D Merritt E. A., Bacon D. J. (1997). "Raster3D Photorealistic Molecular Graphics." Methods in Enzymology 1997, 277 505-524
SCRWL4 Krivov G. G., Shapovalov M. V., Dunbrack R. L. Jr. (2009). "Improved prediction of protein side-chain conformations with SCWRL4." Proteins 2009.
SIFTS
Velankar, S., Dana, J.M., Jacobsen, J., van Ginkel, G., Gane, P.J., Luo, J., Oldfield, T.J., O'Donovan, C., Martin, M.J. and Kleywegt, G.J. (2013) "SIFTS: Structure Integration with Function, Taxonomy and
Sequences resource." Nucleic acids research, 41, D483-489.
SSpro / ACCpro
Cheng J, Randall AZ, Sweredoski MJ, Baldi P. (2005) SCRATCH: a Protein Structure and Structural Feature Prediction Server, Nucleic Acids Research, vol. 33 (web server issue), w72-76, 2005.
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. (2015). "STRING v10: protein-protein interaction networks, integrated over the tree of life." Nucleic Acids Res, 43, D447-52.
SwissDock
Grosdidier A, Zoete V, Michielin O. (2011). "SwissDock, a protein-small molecule docking web service based on EADock DSS." Nucleic Acids Res, 39, W270-7
Grosdidier A, Zoete V, Michielin O. (2011). "Fast docking using the CHARMM force field with EADock DSS." J Comput Chem. 32(10), 2149-59.
TreePack
Xu J, Jiao F, Berger B. (2005). "A tree-decomposition approach to protein structure prediction." Proc IEEE Comput Syst Bioinform Conf, 247-56
Uniclust Mirdita, M., von den Driesch, L., Galiez, C., Martin, M.J., Söding, J., Steinegger, M. (2016) Uniclust databases of clustered and deeply annotated protein sequences and alignments. Nucleic Acids Res, 45, D170–D176.
UniProtKB The UniProt Consortium. (2017) UniProt: the universal protein knowledgebase. Nucleic Acids Res, 45, D158-D169.