2019年蛋白及核酸分析工具.doc

1.蛋白及核酸分析工具/tools/是一个强大的集成生物信息网站。

(1)此网页的包括了预测拓扑Topology prediction•NetNES Leucine-rich nuclear export signals (NES) in eukaryotic proteins（真核蛋白的富含亮氨酸的核输出信号）•PSORT - Prediction of protein subcellular localization （蛋白亚细胞定位）•SecretomeP：Non-classical and leaderless secretion of proteins（蛋白的非经典和无导肽分泌）•TargetP - Prediction of subcellular location （亚细胞定位）•TatP - Twin-arginine signal peptides （精氨酸信号肽）•DAS- Prediction of transmembrane regions in prokaryotes using the Dense Alignment Surface method (Stockholm University) （原核生物中跨膜区预测）•HMMTOP- Prediction of transmembrane helices and topology of proteins (Hungarian Academy of Sciences) （蛋白跨膜螺旋和拓扑结构预测）•PredictProtein- Prediction of transmembrane helix location and topology (Columbia University) （跨膜螺旋定位和拓扑预测）•SOSUI - Prediction of transmembrane regions (Nagoya University, Japan) （跨膜区预测）•TMHMM - Prediction of transmembrane helices in proteins (CBS; Denmark) （跨膜区螺旋预测）•TMpred - Prediction of transmembrane regions and protein orientation (EMBnet-CH) （跨膜区和蛋白定向预测）•TopPred - Topology prediction of membrane proteins (France) （膜蛋白的拓扑预测）最常用的跨膜区预测的两个网站预测跨膜螺旋结构的TMHMM - Prediction of transmembrane helices in proteins (CBS; Denmark)网页为http://www.cbs.dtu.dk/services/TMHMM-2.0/预测跨膜区以及跨膜方向的TMpred - Prediction of transmembrane regions and protein orientation/software/TMPRED_form.html（2）蛋白质一级结构预测Primary structure analysis•ProtParam - Physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, isoelectric point, extinction coefficient, etc.) （蛋白序列的化学参数包括氨基酸、原子组成、等电电、消光系数等）•Compute pI/Mw- Compute the theoretical isoelectric point (pI) and molecular weight (Mw) from a UniProt Knowledgebase entry or for a user sequence （计算理论上的等电点和分子重）•ScanSite pI/Mw - Compute the theoretical pI and Mw, and multiple phosphorylation states （计算理论上的等电点和分子重和多磷酸化状态）•MW, pI, Titration curve - Computes pI, composition and allows to see a titration curve （计算理论上的等电点和组成，可以看滴定曲线）•Scratch Protein Predictor•HeliQuest - A web server to screen sequences with specific alpha-helical properties （一个网站利用专门的alpha螺旋扫描蛋白）•Radar - De novo repeat detection in protein sequences（蛋白序列的重头重复检测）•REP - Searches a protein sequence for repeats （利用重复子搜索蛋白）•REPRO - De novo repeat detection in protein sequences （蛋白序列的重头重复检测）•TRUST - De novo repeat detection in protein sequences （蛋白序列的重头重复检测）•XSTREAM- De novo tandem repeat detection and architecture modeling in protein sequences （蛋白序列的串联重复检测和体系结构建模）•SAPS - Statistical analysis of protein sequences at EMBnet-CH [Also available at EBI] （蛋白统计分析）•Coils- Prediction of coiled coil regions in proteins (Lupas's method) at EMBnet-CH [Also available at PBIL] （蛋白卷曲螺旋预测）•Paircoil - Prediction of coiled coil regions in proteins (Berger's method) （蛋白的卷曲螺旋预测）•Paircoil2 - Prediction of the parallel coiled coil fold from sequence using pairwise residue probabilitis with the Paircoil algorithm. （平行的卷曲螺旋折叠预测）•Multicoil - Prediction of two- and three-stranded coiled coils （二到三股卷曲螺旋预测）•2ZIP - Prediction of Leucine Zippers （亮氨酸拉链预测）•ePESTfind - Identification of PEST regions （PEST区鉴定）•HLA_Bind - Prediction of MHC type I (HLA) peptide binding （HLA肽结合预测）•PEPV AC - Prediction of supertypic MHC binders （亚型MHC结合者预测）•RANKPEP - Prediction of peptide MHC binding（MHC结合预测）•SYFPEITHI - Prediction of MHC type I and II peptide binding （MH C1类和2类结合预测）•ProtScale - Amino acid scale representation (Hydrophobicity, other conformational parameters, etc.) （氨基酸标度呈现）•Drawhca - Draw an HCA (Hydrophobic Cluster Analysis) plot of a protein sequence （蛋白序列亲水性簇分析柱图的绘制）•Peptide Builder （肽构建）•Protein Colourer - Tool for coloring your amino acid sequence （给氨基酸序列上色）•Three To One and One to Three - Tools to convert a three-letter coded amino acid sequence to single letter code and vice versa （从3字母密码子序列到单字母密码子和反过来）•Three-/one-letter amino acid converter- Tool which converts amino acid codes from three-letter to one-letter and vice versa. （转变氨基酸密码子从3字母到1字母或者相反）•Colorseq - Tool to highlight (in red) a selected set of residues in a protein sequence （标亮蛋白序列的选定区域）•PepDraw - peptide primary structure drawing （肽一级结构绘制）•RandSeq - Random protein sequence generator （随机蛋白产生器）（2）蛋白质二级结构Secondary structure prediction•AGADIR - An algorithm to predict the helical content of peptides （肽螺旋量的预测的公式）•APSSP - Advanced Protein Secondary Structure Prediction Server （高等的蛋白二级结构预测服务器）•CFSSP - Chou & Fasman Secondary Structure Prediction Server （二级结构预测服务器）•GOR - Garnier et al, 1996•HNN - Hierarchical Neural Network method (Guermeur, 1997) （分层式的神经网络方法）•HTMSRAP - Helical TransMembrane Segment Rotational Angle Prediction （螺旋跨膜片段旋转角预测）•Jpred - A consensus method for protein secondary structure prediction at University of Dundee （蛋白二级结构预测的一致方法）•JUFO - Protein secondary structure prediction from sequence (neural network) （从序列预测蛋白的二级结构）•NetSurfP - Protein Surface Accessibility and Secondary Structure Predictions （蛋白表明可进入性和二级结构预测）•NetTurnP - Prediction of Beta-turn regions in protein sequences （蛋白序列的Beta转角预测）•nnPredict - University of California at San Francisco (UCSF) （nn预测）不能用•Porter - University College Dublin•PredictProtein - PHDsec, PHDacc, PHDhtm, PHDtopology, PHDthreader, MaxHom, EvalSec from Columbia University （蛋白预测）•Prof - Cascaded Multiple Classifiers for Secondary Structure Prediction （二级结构预测的级联的多样分类）•PSA - BioMolecular Engineering Research Center (BMERC) / Boston•PSIpred - Various protein structure prediction methods at Bloomsbury Centre for Bioinformatics （多样的蛋白结构预测）•SOPMA - Geourjon and Deléage, 1995•Scratch Protein Predictor•DLP-SVM -Domain linker prediction using SVM at Tokyo University of Agriculture and Technology（域连接预测）（3）三级结构分析Tertiary structure Tertiary structure analysis•iMolTalk - An Interactive Protein Structure Analysis Server (currently down)（一个相互作用的蛋白结构分析服务器）•MolTalk - A computational environment for structural bioinformatics （结构生物学的计算环境）•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 proteins•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三级结构预测Tertiary structure predictionHomology modeling （同源模型）•SWISS-MODEL- An automated knowledge-based protein modelling server http://www.expasy.ch/swissmod/SWISS-MODEL.html•CPHmodels - Automated neural-network based protein modelling server•ESyPred3D - Automated homology modeling program using neural networks•Geno3d - Automatic modelling of protein three-dimensional structureThreading （线头）•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 •LOOPP - Sequence to sequence, sequence to structure, and structure to structure alignment •SAM-T08 - HMM-based Protein Structure Prediction•PSIpred - Various protein structure prediction methods (including threading) at Bloomsbury Centre for BioinformaticsAb initio （从头开始）•HMMSTR/Rosetta - Prediction of protein structure from sequence评价三级结构预测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 - Server for Model Quality Estimation•What If - Protein structure analysis program for mutant prediction, structure verification, molecular graphics（四）四级机构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（五）分子模型和可视化工具Molecular modeling and visualization tools•Swiss-PdbViewer - A program to display, analyse and superimpose protein 3D structures •SwissDock - Docking of small ligands into protein active sites with EADock DSS•SwissParam - Topology and parameters for small molecules, for use with CHARMM and GROMAC•Ascalaph Packages•Astex Viewer•Jmol•MarvinSpace - 3D molecule visualization tool•MolMol•MovieMaker - For rapid rendering of protein motions and interactions•PyMol•Rasmol•SRS 3D•VMD•YASARA - Molecular graphics, modeling, simulations and eLearning（六）混乱区预测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（七）序列排列Sequence alignment二元Binary•SIM + LALNVIEW - Alignment of two protein sequences with SIM, results can be viewed with LALNVIEW•LALIGN - Finds multiple matching subsegments in two sequences•Dotlet - A Java applet for sequence comparisons using the dot matrix method多元Multiple•Decrease redundancy - Reduce a set of sequences into a non-redundant set•Nomad (Neighborhood Optimization for Multiple Alignment Discovery) - Ungapped local multiple alignment, optimized for protein sequences, even when distantly related•CLUSTALW [At EBI, PBIL, My Hits or at EMBnet-CH ] •KALIGN - An accurate and fast multiple sequence alignment algorithm [At Karolinska Institute or at EBI]•MAFFT [At Kyushu University, EBI or at MyHits ]•Muscle [At Berkeley or at BioAssist]•T-Coffee [At MyHits , BioAssist or at EBI]•MSA - at Genestream (IGH)•DIALIGN - Multiple sequence alignment based on segment-to-segment comparison, at University of Bielefeld, Germany•Match-Box - at University of Namur, Belgium - at Washington University•Multalin [At GenoToul Bioinfo or at PBIL]•MUSCA - Multiple sequence alignment using pattern discovery, at IBM（八）同源性分析Alignment analysis•AMAS - Analyse Multiply Aligned Sequences•Bork's alignment tools - Various tools to enhance the results of multiple alignments (including consensus building).•CINEMA - Color Interactive Editor for multiple alignments•ESPript - Tool to print a multiple alignment•MaxAlign - Post-processing of alignments by removing sequences (taxa) with many gaps •PhyloGibbs - Gibbs motif sampler incorporating phylogeny and tracking statistics•SV A - Sequence Variability Analyser for multiple alignments•PVS - A protein variability server optimized for conserved epitope discovery•WebLogo - Sequence logos at Berkeley/USA•plogo - Sequence logos at CBS/Denmark•GENIO/logo - Sequence logos at Stuttgart/Germany•SeqLogo - Sequence logos at the Immunomedicine Group, Facultad de Medicina, U.C.M, Spain (The Molecular Immunology Foundation (MIF) does not exist anymore)（九）系统进化分析Phylogenetic analysis•BIONJ - Server for NJ phylogenetic analysis•DendroUPGMA•PHYLIP - Server for phylogenetic analysis using the PHYLIP package•PhyML - Server for ML phylogenetic analysis•Phylogeny.fr - Robust Phylogenetic Analysis For The Non-Specialist•The PhylOgenetic Web Repeater (POWER) - Performs phylogenetic analysis•BlastO - Blast on orthologous groups•Evolutionary Trace Server (TraceSuite II) - Maps evolutionary traces to structures•Phylogenetic programs - List of phylogenetic packages and free servers (PHYLIP pages)（十）生物篇章分析Biological text analysis•AcroMed - A computer generated database of biomedical acronyms and the associated long forms extracted from the recent Medline abstracts •BioMinT - Mining the biomedical literature •GPSDB - Gene and Protein Synonym DataBase•Medline Ranker•The Miner Suite - of bioinformatic software packages and data analysis•XplorMed - Explore a set of abstracts derived from a bibliographic search in MEDLINE（十一）统计工具Statistical tools•pROC - A package (R, S+) to visualize, smooth and compare receiver operating characteristic (ROC curves/点服务，有TMPRED Transmembrane regions detection 二级跨膜区预测。