Terms and conditions


Use of the SPASE webserver (the "Software") is subject to the following terms and conditions:

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.


The SPASE webserver employs the following tools:

  • Pymol
  • PDBFixer
  • ProteinMPNN
  • Protein-Sol
  • ESMFold
  • Aggrescan3D (A3D)

    References:

    Pymol:

  • The PyMOL Molecular Graphics System, Version 2.5.0 Schrödinger, LLC.

    PDBFixer:

  • github.com/openmm/pdbfixer

    ProteinMPNN:

  • Dauparas J, Anishchenko I, Bennett N, Bai H, Ragotte RJ, Milles LF, Wicky BIM, Courbet A, de Haas RJ, Bethel N, Leung PJY, Huddy TF, Pellock S, Tischer D, Chan F, Koepnick B, Nguyen H, Kang A, Sankaran B, Bera AK, King NP, Baker D. Robust deep learning-based protein sequence design using ProteinMPNN. Science. 2022 Oct 7;378(6615):49-56. doi: 10.1126/science.add2187. Epub 2022 Sep 15. PMID: 36108050; PMCID: PMC9997061.

    Protein-Sol:

  • Hebditch M, Carballo-Amador MA, Charonis S, Curtis R, Warwicker J. Protein-Sol: a web tool for predicting protein solubility from sequence. Bioinformatics. 2017 Oct 1;33(19):3098-3100. doi: 10.1093/bioinformatics/btx345. PMID: 28575391; PMCID: PMC5870856.

    ESMFold:

  • Lin Z, Akin H, Rao R, Hie B, Zhu Z, Lu W, Smetanin N, Verkuil R, Kabeli O, Shmueli Y, Dos Santos Costa A, Fazel-Zarandi M, Sercu T, Candido S, Rives A. Evolutionary-scale prediction of atomic-level protein structure with a language model. Science. 2023 Mar 17;379(6637):1123-1130. doi: 10.1126/science.ade2574. Epub 2023 Mar 16. PMID: 36927031.

    Aggrescan3D:

  • Conchillo-Solé O, de Groot NS, Avilés FX, Vendrell J, Daura X, Ventura S. AGGRESCAN: a server for the prediction and evaluation of "hot spots" of aggregation in polypeptides. BMC Bioinformatics. 2007 Feb 27;8:65. doi: 10.1186/1471-2105-8-65. PMID: 17324296; PMCID: PMC1828741.

  • de Groot NS, Castillo V, Graña-Montes R, Ventura S. AGGRESCAN: method, application, and perspectives for drug design. Methods Mol Biol. 2012;819:199-220. doi: 10.1007/978-1-61779-465-0_14. PMID: 22183539.