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PROVE. Reference: Deviations from standard atomic volumes as a quality measure for protein crystal structures, Pontius J, Richelle J, Wodak SJ. 1996. PROCHECK source information. Result analysis. from Protein Structures. Original references. WHATCHECK documentation and source.
- Usage
UCLA-DOE LAB — SAVES v6.1. Usages - Number of Jobs (not...
- Structure Validation Server
Go here to submit a structure to SAVES.
- Usage
Jul 15, 2021 · SAVES is an interactive validation server for 5 programs commonly used in protein structure validation. It runs since 2004 and can be accessed through a dashboard screen with various tools and references.
- Methods
- Input Formats
- References
SSpro
SSpro is a server for protein secondary structure prediction based on protein evolutionaryinformation (sequence homology) and homologous protein's secondary structure (structure homology).For a detailed explanation of the methods, please refer to the references listed at the bottomof this page. SSpro currently achieves a performance exceeding 84% correctly classified residueson proteins with no homologs in the PDB and in the range of 87.8% to 98.7% correctly classified residues on proteinswhe...
SSpro8
SSpro8 is an extension to SSpro. Instead of using three classes (helix, strand and the rest)to assign the secondary structure of a protein, SSpro8 adopts the full DSSP 8-class outputclassification: 1. H: alpha-helix 2. G: 3-10-helix 3. I: pi-helix (extremely rare) 4. E: extended strand 5. B: beta-bridge 6. T: turn 7. S: bend 8. C: the rest For a detailed description of the tests performed on SSpro8, see the references. The overallperformance of the system currently online is approximately 72%...
ABTMpro
ABTMpro is a server that predicts whether a given protein sequence is a transmembrane protein. If the given protein sequence is a transmembrane protein, ABTMpro further predicts the probabilities of the protein being an alpha helical transmembrane protein or a Beta Barrel transmembrane protein. The prediction framework consists of a Support Vector Machine, which utilizes features such as amino acid composition and properties, reduced alphabet composition, predicted secondary structure, evolut...
Email
Your email address, the place where the prediction will be delivered.NOTE: Check that you typed your address correctly. Approximately 5% ofthe queries handled by SSpro 1.0 didn't receive an answer because ofincorrect typing.
Query name
An optional name for your query. We strongly suggest that you use one,especially if sending more than one query. The order in which you sendyour queries may not correspond to the order in which you receive theanswers.
Input sequence
The sequence of amino acids: 1. A bare sequence is accepted. Please no FASTA format. 2. Spaces, newlines and tabs will be ignored, so feel free to have them in your query. 3. Letters not corresponding to any amino acid will be treated as X. 4. Non alphabetical chars will cause the rejection of the query. 5. Only 1 letter amino acid code accepted. Please do not send nucleotide sequences. If so, A will be treated as Alanine, C as Cysteine, etc...
For the server and SSpro/ACCpro 4.0 software package, please refer to: J. Cheng, A. Randall, M. Sweredoski, P. Baldi, SCRATCH: a Protein Structure and Structural Feature Prediction Server, Nucleic Acids Research, vol. 33 (web server issue), w72-76, 2005.[PDF][PDF at NAR website][Download SSpro/ACCpro 4.0] For the previous version of the SSpro/ACCpr...
3 days ago · UCLA-DOE LAB — SAVES v6.1. Usages - Number of Jobs (not individual programs running) New Job Thursday, September 26, 2024 : 565 jobs up to 10:19 am America/Los_Angeles.
Go here to submit a structure to SAVES.
You can use UCLA-DOE LAB — SAVES v6.0 (https://saves.mbi.ucla.edu/). It is a server that makes an evaluation of the 3D structure of proteins using 5 different servers: WHATCHEK,...
People also ask
What is saves & how does it work?
What is the ultimate goal of structure prediction?
What is a prediction framework?
Jan 1, 2022 · One such server is SAVES, hosted by DOE-MBI. The server uses ERRAT, 37 VERIFY 3D, 38 PROVE, 39 PROCHECK, 40 and WHAT CHECK 41 tools to evaluate the input model structure. ERRAT quality gives the percentage of protein for which the calculated error values are less than the 95% rejection limit.
