How to cite us?

  • The molecular dynamics simulations and related data from:
    Aliaa E. Ali, Li-Li Li, Michael J. Courtney, Olli T. Pentikäinen, Pekka A. Postila (2024), Atomistic Simulations Reveal Impacts of Missense Mutations on the Structure and Function of SynGAP1, Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae458, DOI: 10.1093/bib/bbae458
  • SynGAP Missense Server:
    Aliaa E. Ali, Henna-Riikka Otranen, Michael J. Courtney, Olli T. Pentikäinen, Pekka A. Postila (2024), Untitled manuscript presenting the SynGAP Missense Server. Manuscript under preparation.

Please cite the original publications on the used databases, software and online tools

The data included in the SGM server is acquired from academical research, relying on academic licenses; accordingly, respect the original licenses, if using the server data for commercial activities (disclaimer). Please, note that the linked info on licenses could be outdated or inaccurate and should be verified by the user.

AlphaMissense

  • Article: Jun Cheng, Guido Novati, Joshua Pan, Clare Bycroft, Akvilė Žemgulytė, Taylor Applebaum, Alexander Pritzel, Lai Hong Wong, Michal Zielinski, Tobias Sargeant, Rosalia G Schneider, Andrew W Senior, John Jumper, Demis Hassabis, Pushmeet Kohli, Žiga Avsec. Accurate proteome-wide missense variant effect prediction with AlphaMissense. Science. 2023 Sep 22;381(6664):eadg7492.
  • Purpose: Missense mutation pathogenicity predictions.
  • DOI: 10.1126/science.adg7492
  • PMID: 37733863/
  • Info on license: https://alphamissense.hegelab.org/

AlphaFold2 (via AlphaFold Database)

  • Article: John Jumper, Richard Evans, Alexander Pritzel, Tim Green, Michael Figurnov, Olaf Ronneberger, Kathryn Tunyasuvunakool, Russ Bates, Augustin Žídek, Anna Potapenko, Alex Bridgland, Clemens Meyer, Simon A A Kohl, Andrew J Ballard, Andrew Cowie, Bernardino Romera-Paredes, Stanislav Nikolov, Rishub Jain, Jonas Adler, Trevor Back, Stig Petersen, David Reiman, Ellen Clancy, Michal Zielinski, Martin Steinegger, Michalina Pacholska, Tamas Berghammer, Sebastian Bodenstein, David Silver, Oriol Vinyals, Andrew W Senior, Koray Kavukcuoglu, Pushmeet Kohli, Demis Hassabis. Highly accurate protein structure prediction with AlphaFold. Nature. 2021 Aug;596(7873):583-589.
  • Purpose: N-terminal 3D model for SynGAP used as a basis for in silico mutagenesis.
  • DOI: 10.1038/s41586-021-03819-2
  • PMID: 34265844/
  • PMCID: PMC8371605/
  • Info on license: https://alphafold.ebi.ac.uk/

AlphaFold3 (via AlphaFold Server)

  • Article: Josh Abramson, Jonas Adler, Jack Dunger, Richard Evans, Tim Green, Alexander Pritzel, Olaf Ronneberger, Lindsay Willmore, Andrew J Ballard, Joshua Bambrick, Sebastian W Bodenstein, David A Evans, Chia-Chun Hung, Michael O'Neill, David Reiman, Kathryn Tunyasuvunakool, Zachary Wu, Akvilė Žemgulytė, Eirini Arvaniti, Charles Beattie, Ottavia Bertolli, Alex Bridgland, Alexey Cherepanov, Miles Congreve, Alexander I Cowen-Rivers, Andrew Cowie, Michael Figurnov, Fabian B Fuchs, Hannah Gladman, Rishub Jain, Yousuf A Khan, Caroline M R Low, Kuba Perlin, Anna Potapenko, Pascal Savy, Sukhdeep Singh, Adrian Stecula, Ashok Thillaisundaram, Catherine Tong, Sergei Yakneen, Ellen D Zhong, Michal Zielinski, Augustin Žídek, Victor Bapst, Pushmeet Kohli, Max Jaderberg, Demis Hassabis, John M Jumper. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature. 2024 Jun;630(8016):493-500.
  • Purpose: CC domain 3D model for SynGAP used as a basis for in silico mutagenesis.
  • DOI: 10.1038/s41586-024-07487-w
  • PMID: 38718835/
  • PMCID: PMC11168924/
  • Info on license: https://alphafoldserver.com/output-terms

AMBER22 and AmberTools22

  • D.A. Case, H.M. Aktulga, K. Belfon, I.Y. Ben-Shalom, J.T. Berryman, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, G.A. Cisneros, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, G. Giambasu, M.K. Gilson, H. Gohlke, A.W. Goetz, R. Harris, S. Izadi, S.A. Izmailov, K. Kasavajhala, M.C. Kaymak, E. King, A. Kovalenko, T. Kurtzman, T.S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, M. Machado, V. Man, M. Manathunga, K.M. Merz, Y. Miao, O. Mikhailovskii, G. Monard, H. Nguyen, K.A. O'Hearn, A. Onufriev, F. Pan, S. Pantano, R. Qi, A. Rahnamoun, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, A. Shajan, J. Shen, C.L. Simmerling, N.R. Skrynnikov, J. Smith, J. Swails, R.C. Walker, J. Wang, J. Wang, H. Wei, R.M. Wolf, X. Wu, Y. Xiong, Y. Xue, D.M. York, S. Zhao, and P.A. Kollman (2022), Amber 2022, University of California, San Francisco.
  • Article: David A Case, Hasan Metin Aktulga, Kellon Belfon, David S Cerutti, G Andrés Cisneros, Vinícius Wilian D Cruzeiro, Negin Forouzesh, Timothy J Giese, Andreas W Götz, Holger Gohlke, Saeed Izadi, Koushik Kasavajhala, Mehmet C Kaymak, Edward King, Tom Kurtzman, Tai-Sung Lee, Pengfei Li, Jian Liu, Tyler Luchko, Ray Luo, Madushanka Manathunga, Matias R Machado, Hai Minh Nguyen, Kurt A O'Hearn, Alexey V Onufriev, Feng Pan, Sergio Pantano, Ruxi Qi, Ali Rahnamoun, Ali Risheh, Stephan Schott-Verdugo, Akhil Shajan, Jason Swails, Junmei Wang, Haixin Wei, Xiongwu Wu, Yongxian Wu, Shi Zhang, Shiji Zhao, Qiang Zhu, Thomas E Cheatham 3rd, Daniel R Roe, Adrian Roitberg, Carlos Simmerling, Darrin M York, Maria C Nagan, Kenneth M Merz Jr. AmberTools. J Chem Inf Model. 2023 Oct 23;63(20):6183-6191.
  • Purpose: MD simulation software used for probing the SynGAP-solvent systems.
  • Dependencies: AlphaFold2, AlphaFold3, MODELLER, and AMBERTOOLS.
  • Info: https://ambermd.org/CiteAmber.php
  • Info on licenses: https://ambermd.org/#Amber22, https://ambermd.org/#AmberTools

ClinVar

  • Article: Melissa J Landrum, Jennifer M Lee, George R Riley, Wonhee Jang, Wendy S Rubinstein, Deanna M Church, Donna R Maglott. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 2014 Jan;42(Database issue):D980-5.
  • Purpose: A source for missense variant information.
  • DOI: 10.1093/nar/gkt1113
  • PMID: 24234437/
  • PMCID: PMC3965032/
  • Info on license: https://www.ncbi.nlm.nih.gov/clinvar/intro/

ESM1b

FoldX

  • Article: Joost Schymkowitz, Jesper Borg, Francois Stricher, Robby Nys, Frederic Rousseau, Luis Serrano. The FoldX web server: an online force field. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W382-8.
  • Purpose: Folding stability calculations estimating the pathogenicity of missense mutations.
  • Dependencies: AlphaFold2, MODELLER, AMBER and AMBERTOOLS.
  • DOI: 10.1093/nar/gki387
  • PMID: 15980494/
  • PMCID: PMC1160148
  • Info on license: https://foldxsuite.crg.eu/licensing-and-services

FATHMM

  • Article: Hashem A Shihab, Julian Gough, David N Cooper, Peter D Stenson, Gary L A Barker, Keith J Edwards, Ian N M Day, Tom R Gaunt. Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models. Hum Mutat. 2013 Jan;34(1):57-65.
  • Purpose: Missense mutation pathogenicity predictions.
  • DOI: 10.1002/humu.22225
  • PMID: 23033316/
  • PMCID: PMC3558800/
  • Info on license: https://fathmm.biocompute.org.uk/downloads.html

gnomAD

  • Article: Konrad J Karczewski, Laurent C Francioli, Grace Tiao, Beryl B Cummings, Jessica Alföldi, Qingbo Wang, Ryan L Collins, Kristen M Laricchia, Andrea Ganna, Daniel P Birnbaum, Laura D Gauthier, Harrison Brand, Matthew Solomonson, Nicholas A Watts, Daniel Rhodes, Moriel Singer-Berk, Eleina M England, Eleanor G Seaby, Jack A Kosmicki, Raymond K Walters, Katherine Tashman, Yossi Farjoun, Eric Banks, Timothy Poterba, Arcturus Wang, Cotton Seed, Nicola Whiffin, Jessica X Chong, Kaitlin E Samocha, Emma Pierce-Hoffman, Zachary Zappala, Anne H O'Donnell-Luria, Eric Vallabh Minikel, Ben Weisburd, Monkol Lek, James S Ware, Christopher Vittal, Irina M Armean, Louis Bergelson, Kristian Cibulskis, Kristen M Connolly, Miguel Covarrubias, Stacey Donnelly, Steven Ferriera, Stacey Gabriel, Jeff Gentry, Namrata Gupta, Thibault Jeandet, Diane Kaplan, Christopher Llanwarne, Ruchi Munshi, Sam Novod, Nikelle Petrillo, David Roazen, Valentin Ruano-Rubio, Andrea Saltzman, Molly Schleicher, Jose Soto, Kathleen Tibbetts, Charlotte Tolonen, Gordon Wade, Michael E Talkowski; Genome Aggregation Database Consortium; Benjamin M Neale, Mark J Daly, Daniel G MacArthur. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature. 2020 May;581(7809):434-443.
  • Purpose: A source for missense variant information.
  • DOI: 10.1038/s41586-020-2308-7
  • PMID: 32461654/
  • PMCID: PMC7334197
  • Info on license: https://gnomad.broadinstitute.org/terms

MODELLER10.3

Mol*Viewer

  • Article: David Sehnal, Sebastian Bittrich, Mandar Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K Burley, Jaroslav Koča, Alexander S Rose. Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures.Nucleic Acids Res. 2021 Jul 2;49(W1):W431-W437
  • Purpose: The software plugin is embedded in the 3DViewer.
  • DOI: 10.1093/nar/gkab314
  • PMID: 33956157/
  • PMCID: PMC8262734/
  • Info on license: https://molstar.org/terms-of-use.html

PolyPhen-2

PremPS

PROVEAN

Rosetta

  • Article: Frenz B, Lewis SM, King I, DiMaio F, Park H, Song Y. Prediction of Protein Mutational Free Energy: Benchmark and Sampling Improvements Increase Classification Accuracy. Front Bioeng Biotechnol. 2020;8.
  • Purpose: Folding stability calculations estimating the pathogenicity of missense mutations.
  • Dependencies: AlphaFold2, AlphaFold3, MODELLER, AMBER and AMBERTOOLS.
  • DOI: 10.3389/fbioe.2020.558247
  • Info on license: www.rosettacommons.org/software/license-and-download

Foldetta

  • Article: Gerasimavicius L, Livesey BJ, Marsh JA. Correspondence between functional scores from deep mutational scans and predicted effects on protein stability. Protein Science. 2023;32(7).
  • Purpose: Folding stability calculations estimating the pathogenicity of missense mutations.
  • Dependencies: FoldX, Rosetta
  • DOI: 10.1002/pro.4688
  • PMID: 37243972
  • PMCID: PMC10273344

SIFT

  • Article: Ngak-Leng Sim, Prateek Kumar, Jing Hu, Steven Henikoff, Georg Schneider, Pauline C Ng. SIFT web server: predicting effects of amino acid substitutions on proteins. Nucleic Acids Res. 2012 Jul;40(Web Server issue):W452-7.
  • Purpose: Missense mutation pathogenicity predictions.
  • DOI: 10.1093/nar/gks539
  • PMID: 22689647
  • PMCID: PMC3394338
  • Info on license: PMC3394338/

REVEL

  • Article: Nilah M Ioannidis, Joseph H Rothstein, Vikas Pejaver, Sumit Middha, Shannon K McDonnell, Saurabh Baheti, Anthony Musolf, Qing Li, Emily Holzinger, Danielle Karyadi, Lisa A Cannon-Albright, Craig C Teerlink, Janet L Stanford, William B Isaacs, Jianfeng Xu 13, Kathleen A Cooney, Ethan M Lange, Johanna Schleutker, John D Carpten, Isaac J Powell, Olivier Cussenot, Geraldine Cancel-Tassin, Graham G Giles, Robert J MacInnis, Christiane Maier, Chih-Lin Hsieh, Fredrik Wiklund, William J Catalona, William D Foulkes, Diptasri Mandal, Rosalind A Eeles, Zsofia Kote-Jarai, Carlos D Bustamante, Daniel J Schaid, Trevor Hastie, Elaine A Ostrander, Joan E Bailey-Wilson, Predrag Radivojac, Stephen N Thibodeau, Alice S Whittemore, Weiva Sieh. REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants. Am J Hum Genet. 2016 Sep 22;99(4):877–885.
  • Purpose: Missense mutation pathogenicity predictions.
  • Dependencies: SiPhy, phyloP, phastCons, MutPred, FATHMM v2.3, VEST 3.0, PolyPhen-2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, and GERP++.
  • DOI: 10.1016/j.ajhg.2016.08.016
  • PMID: 27666373
  • PMCID: PMC5065685
  • Info on license: https://sites.google.com/site/revelgenomics/downloads

Top


The image was created with the assistance of DALL·E 3 via MS Copilot.