Institute of Enzymology Servers
Institute of Enzymology Servers provide computational analyses for protein structure characterization and prediction, focusing on transmembrane topology, stabilization centers, intrinsic disorder, cysteine redox states, and non-covalent cross-links.
Key Features:
- Transmembrane Protein Structure Prediction (HMMTOP): HMMTOP predicts helical transmembrane segments and their topologies and incorporates segment localization data to enhance prediction accuracy.
- DAS-TMfilter (Dense Alignment Surface refinement): DAS-TMfilter refines the Dense Alignment Surface method to reduce false positives in non-transmembrane sequences while maintaining high sensitivity and selectivity.
- Stabilization Center Identification (SCIDE): SCIDE identifies stabilization centers from known protein structures using cooperative long-range interactions.
- Neural Network-based Stabilization Center Prediction: Artificial neural network algorithms predict stabilization-center residues and incorporate evolutionary information to improve accuracy.
- Protein Disorder Prediction (IUPred): IUPred estimates pairwise interaction energy from amino acid composition to distinguish folded regions from intrinsically disordered regions in protein sequences.
- Cysteine Redox State Analysis (CYSREDOX): CYSREDOX reports the covalent redox states of cysteines within proteins for analysis of redox regulation.
- Non-Covalent Cross-Link Prediction (SCPRED): SCPRED identifies residues involved in non-covalent cross-links that contribute to protein structural stability.
- Transmembrane Protein Database (PDB_TM): PDB_TM collects transmembrane proteins with known structures, uses the TMDET algorithm to determine membrane-spanning regions, and is updated weekly.
Scientific Applications:
- Protein Stability Analysis: SCIDE, SCPRED, and IUPred enable analysis of stabilization centers, cross-links, and disorder to study protein stability and misfolding-related disease mechanisms.
- Transmembrane Protein Research: HMMTOP, DAS-TMfilter, and PDB_TM support accurate identification and characterization of transmembrane regions relevant to membrane protein structure-function studies and drug targeting.
- Structural Biology Studies: Identification of stabilization centers and structural features supports investigations into protein folding mechanisms and evolutionary conservation of structural elements.
Methodology:
Methods explicitly include artificial neural networks, quadratic forms in amino acid composition, pairwise interaction energy estimation, Dense Alignment Surface refinement (DAS-TMfilter), the TMDET algorithm, and structural analysis algorithms.
Topics
Details
- Tool Type:
- web application
- Operating Systems:
- Linux, Windows, Mac
- Added:
- 3/25/2017
- Last Updated:
- 11/25/2024
Operations
Data Inputs & Outputs
Protein fold recognition
Publications
Tusnády GE, Dosztányi Z, Simon I. Transmembrane proteins in the Protein Data Bank: identification and classification. Bioinformatics. 2004;20(17):2964-2972. doi:10.1093/bioinformatics/bth340. PMID:15180935.
Dosztanyi Z, Csizmok V, Tompa P, Simon I. IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics. 2005;21(16):3433-3434. doi:10.1093/bioinformatics/bti541. PMID:15955779.
Dosztányi Z, Magyar C, Tusnády G, Simon I. SCide: identification of stabilization centers in proteins. Bioinformatics. 2003;19(7):899-900. doi:10.1093/bioinformatics/btg110. PMID:12724305.
Dosztanyi Z. Servers for sequence-structure relationship analysis and prediction. Nucleic Acids Research. 2003;31(13):3359-3363. doi:10.1093/nar/gkg589. PMID:12824327. PMCID:PMC168995.
Tusnády GE, Dosztányi Z, Simon I. TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates. Bioinformatics. 2004;21(7):1276-1277. doi:10.1093/bioinformatics/bti121. PMID:15539454.
Tusnády GE, Simon I. Principles governing amino acid composition of integral membrane proteins: application to topology prediction 1 1Edited by J. Thornton. Journal of Molecular Biology. 1998;283(2):489-506. doi:10.1006/jmbi.1998.2107. PMID:9769220.
Dosztányi Z, Csizmók V, Tompa P, Simon I. The Pairwise Energy Content Estimated from Amino Acid Composition Discriminates between Folded and Intrinsically Unstructured Proteins. Journal of Molecular Biology. 2005;347(4):827-839. doi:10.1016/j.jmb.2005.01.071. PMID:15769473.
Gromiha MM, Pujadas G, Magyar C, Selvaraj S, Simon I. Locating the stabilizing residues in (α/β)<sub>8</sub> barrel proteins based on hydrophobicity, long‐range interactions, and sequence conservation. Proteins: Structure, Function, and Bioinformatics. 2004;55(2):316-329. doi:10.1002/prot.20052. PMID:15048825.
Tusn dy GbE. BiSearch: primer-design and search tool for PCR on bisulfite-treated genomes. Nucleic Acids Research. 2005;33(1):e9-e9. doi:10.1093/nar/gni012. PMID:15653630. PMCID:PMC546182.
Tusnády GE, Simon I. The HMMTOP transmembrane topology prediction server. Bioinformatics. 2001;17(9):849-850. doi:10.1093/bioinformatics/17.9.849. PMID:11590105.
Cserzö M, Eisenhaber F, Eisenhaber B, Simon I. On filtering false positive transmembrane protein predictions. Protein Engineering, Design and Selection. 2002;15(9):745-752. doi:10.1093/protein/15.9.745. PMID:12456873.
Tusnady GE. PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank. Nucleic Acids Research. 2004;33(Database issue):D275-D278. doi:10.1093/nar/gki002. PMID:15608195. PMCID:PMC539956.
Dosztányi Z, Fiser A, Simon I. Stabilization centers in proteins:Identification, characterization and predictions. Journal of Molecular Biology. 1997;272(4):597-612. doi:10.1006/jmbi.1997.1242. PMID:9325115.