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【求助/交流】蛋白质功能域分析求教 已有1人参与
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如题，请教用什么软件可以分析蛋白质的功能域，还有疏水性、跨膜结构、3D建模之类的呢， [ Last edited by finding1371 on 2010-8-7 at 11:16 ] |
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finding1371(金币+5):谢谢您提示，呵呵 2010-08-07 11:16:25
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关于蛋白质方面的ExPASy 收录的很多。http://www.expasy.ch/tools/ 下面是一个列表，我想你可你根据你的喜好，还有是否收费，进行选择： Topology prediction * NetNES Leucine-rich nuclear export signals (NES) in eukaryotic proteins * PSORT - Prediction of protein subcellular localization * SecretomeP - Non-classical and leaderless secretion of proteins * TargetP - Prediction of subcellular location * TatP - Twin-arginine signal peptides * DAS - Prediction of transmembrane regions in prokaryotes using the Dense Alignment Surface method (Stockholm University) * HMMTOP - Prediction of transmembrane helices and topology of proteins (Hungarian Academy of Sciences) * PredictProtein - Prediction of transmembrane helix location and topology (Columbia University) * SOSUI - Prediction of transmembrane regions (Nagoya University, Japan) * TMAP - Transmembrane detection based on multiple sequence alignment (Karolinska Institut; Sweden) * TMHMM - Prediction of transmembrane helices in proteins (CBS; Denmark) * TMpred SIB - Prediction of transmembrane regions and protein orientation (EMBnet-CH) * TopPred - Topology prediction of membrane proteins (France) Primary structure analysis * ProtParam local - Physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, isoelectric point, extinction coefficient, etc.) * Compute pI/Mw local - Compute the theoretical isoelectric point (pI) and molecular weight (Mw) from a UniProt Knowledgebase entry or for a user sequence * ScanSite pI/Mw - Compute the theoretical pI and Mw, and multiple phosphorylation states * MW, pI, Titration curve - Computes pI, composition and allows to see a titration curve * HeliQuest - A web server to screen sequences with specific alpha-helical properties * Radar - De novo repeat detection in protein sequences * REP - Searches a protein sequence for repeats * REPRO - De novo repeat detection in protein sequences * TRUST - De novo repeat detection in protein sequences * XSTREAM - De novo tandem repeat detection and architecture modeling in protein sequences * SAPS SIB - Statistical analysis of protein sequences at EMBnet-CH [Also available at EBI] * Coils SIB - Prediction of coiled coil regions in proteins (Lupas's method) at EMBnet-CH [Also available at PBIL] * Paircoil - Prediction of coiled coil regions in proteins (Berger's method) * Paircoil2 - Prediction of the parallel coiled coil fold from sequence using pairwise residue probabilitis with the Paircoil algorithm. * Multicoil - Prediction of two- and three-stranded coiled coils * 2ZIP - Prediction of Leucine Zippers * ePESTfind - Identification of PEST regions * HLA_Bind - Prediction of MHC type I (HLA) peptide binding * PEPVAC - Prediction of supertypic MHC binders * RANKPEP - Prediction of peptide MHC binding * SYFPEITHI - Prediction of MHC type I and II peptide binding * ProtScale local - Amino acid scale representation (Hydrophobicity, other conformational parameters, etc.) * Drawhca - Draw an HCA (Hydrophobic Cluster Analysis) plot of a protein sequence * Peptide Builder * Protein Colourer - Tool for coloring your amino acid sequence * Three To One and One to Three - Tools to convert a three-letter coded amino acid sequence to single letter code and vice versa * Three-/one-letter amino acid converter - Tool which converts amino acid codes from three-letter to one-letter and vice versa. * Colorseq - Tool to highlight (in red) a selected set of residues in a protein sequence * HelixWheel / HelixDraw - Representations of a protein fragment as a helical wheel * RandSeq local - Random protein sequence generator Secondary structure prediction * AGADIR - An algorithm to predict the helical content of peptides * APSSP - Advanced Protein Secondary Structure Prediction Server * CFSSP - Chou & Fasman Secondary Structure Prediction Server * GOR - Garnier et al, 1996 * HNN - Hierarchical Neural Network method (Guermeur, 1997) * HTMSRAP - Helical TransMembrane Segment Rotational Angle Prediction * Jpred - A consensus method for protein secondary structure prediction at University of Dundee * JUFO - Protein secondary structure prediction from sequence (neural network) * NetSurfP - Protein Surface Accessibility and Secondary Structure Predictions new * nnPredict - University of California at San Francisco (UCSF) * Porter - University College Dublin * PredictProtein - PHDsec, PHDacc, PHDhtm, PHDtopology, PHDthreader, MaxHom, EvalSec from Columbia University * Prof - Cascaded Multiple Classifiers for Secondary Structure Prediction * PSA - BioMolecular Engineering Research Center (BMERC) / Boston * PSIpred - Various protein structure prediction methods at Brunel University * SOPMA - Geourjon and Deléage, 1995 * SSpro - Secondary structure prediction using bidirectional recurrent neural networks at University of California * DLP-SVM - Domain linker prediction using SVM at Tokyo University of Agriculture and Technology Tertiary structure Tertiary structure analysis * iMolTalk - An Interactive Protein Structure Analysis Server * MolTalk - A computational environment for structural bioinformatics * COPS - Navigation through fold space and the instantaneous visualization of pairwise structure similarities * PoPMuSiC - Prediction of thermodynamic stability changes upon point mutations; design of modified proteinsnew * Seq2Struct - A web resource for the identification of sequence-structure links * STRAP - A structural alignment program for proteins * TLSMD - TLS (Translation/Libration/Screw) Motion Determination * TopMatch-web - Protein structure comparison Tertiary structure prediction Homology modeling * SWISS-MODEL local - An automated knowledge-based protein modelling server * 3Djigsaw - Three-dimensional models for proteins based on homologues of known structure * CPHmodels - Automated neural-network based protein modelling server * ESyPred3D - Automated homology modeling program using neural networks * Geno3d - Automatic modelling of protein three-dimensional structure * SDSC1 - Protein Structure Homology Modeling Server * Phyre (Successor of 3D-PSSM) - Automated 3D model building using profile-profile matching and secondary structure * Fugue - Sequence-structure homology recognition * HHpred - Protein homology detection and structure prediction by HMM-HMM comparison * Libellula - Neural network approach to evaluate fold recognition results * LOOPP - Sequence to sequence, sequence to structure, and structure to structure alignment * SAM-T02 - HMM-based Protein Structure Prediction * Threader - Protein fold recognition * SWEET - Constructing 3D models of saccharides from their sequences Ab initio * HMMSTR/Rosetta - Prediction of protein structure from sequence Assessing tertiary structure prediction * Anolea - Atomic Non-Local Environment Assessment * LiveBench - Continuous Benchmarking of Structure Prediction Servers * NQ-Flipper - Validation and correction of asparagine and glutamine side-chain amide rotamers in protein structures solved by X-ray crystallography * PROCHECK - Verification of the stereochemical quality of a protein structure * ProSA-web - Recognition of errors in 3D structures of proteins * QMEAN local - Server for Model Quality Estimation * What If - Protein structure analysis program for mutant prediction, structure verification, molecular graphics Quaternary structure * MakeMultimer - Reconstruction of multimeric molecules present in crystals * EBI PISA - Protein Interfaces, Surfaces and Assemblies * PQS - Protein Quaternary Structure Query form at the EBI * ProtBud - Comparison of asymmetric units and biological units from PDB and PQS Molecular modeling and visualization tools * Swiss-PdbViewer local - A program to display, analyse and superimpose protein 3D structures * Ascalaph Packages * Astex Viewer * Jmol * MarvinSpace - 3D molecule visualization toolnew * MolMol * MovieMaker - For rapid rendering of protein motions and interactions * PyMol * Rasmol * SRS 3D new * VMD * YASARA - Molecular graphics, modeling, simulations and eLearning Prediction of disordered regions * DisEMBL - Protein disorder prediction * GlobPlot - Protein disorder/order/globularity/domain predictor * MeDor - Metaserver or Disorder * POODLE - Prediction Of Order and Disorder by machine LEarning * List of Protein Disorder Predictors |
2楼2010-08-07 10:21:50