1、1.蛋白及核酸分析工具/tools/是一個強大的集成生物信息網站。（1）此網頁的包括了預測拓撲Topology predictio n?NetNES Leuci ne-rich nuclear export sig nals （NES） in eukaryotic protei ns （真核蛋白的富含 亮氨酸的核輸出信號）?PSORT - Predicti on of prote in subcellular localizati on（蛋白亞纟田胞定位）?SecretomeP : Non-classical and leaderless secreti

2、on of proteins （蛋白的非經典和無導肽 分泌）?TargetP - Prediction of subcellular locatio n（亞細胞定位）?TatP - Twin-arginine sig nal peptides（精氨酸信號肽）?DAS - Prediction of transmembrane regions in prokaryotes using the Dense Alignment Surface method （Stockholm Un iversity）（原核生物中跨膜區預測）?HMMTOP - Prediction of transmembrane

3、 helices and topology of proteins （Hungarian Academy of Scien ces）（蛋白跨膜螺旋和拓撲結構預測）?PredictProte in - Predict ion of tran smembra ne helix locati on and topology （Columbia Uni versity）（跨膜螺旋定位和拓撲預測）?SOSUI - Prediction of tran smembra ne regio ns （Nagoya Un iversity, Japa n）（跨膜區預測）?TMHMM - Predictio n o

4、f tran smembra ne helices in protei ns （CBS; De nm ark）（跨膜區螺旋 預測）?TMpred- Prediction of transmembrane regions and protein orientation （EMBnet-CH） （跨膜區和蛋白定向預測）?TopPred - Topology predict ion of membra ne prote ins （Fra nee）（膜蛋白的拓扌卜預測）最常用的跨膜區預測的兩個網站預測跨膜螺旋結構的TMHMM - Prediction of transmembrane helices

5、in proteins （CBS; Denmark）網頁為http:/www.cbs.dtu.dk/services/TMHMM-2.0/預測跨膜區以及跨膜方向 的TMpred - Predictio n of tran smembra ne regi ons and protein orie ntati on/software/TMPRED form.html（2）蛋白質一級結構預測 Primary structure analysis?ProtParam - Physico-chemical parameters of a prote in s

6、eque nee （am ino-acid and atomic compositi on s, isoelectric point, ext inction coefficie nt, etc.）（蛋白序列的化學參數包括氨基酸、原子組成、等電電、消光系數等）?Compute pl/Mw - Compute the theoretical isoelectric point （pl） and molecular weight （Mw） from a Un iProt Kno wledgebase entry or for a user seque nee（計算理論上的等電點和分子重）?Scan

7、Site pl/Mw - Compute the theoretical pl and Mw, and multiple phosphorylation states（計算理論上的等電點和分子重和多磷酸化狀態）?MW, pl, Titration curve - Computes pl, composition and allows to see a titration curve （計 算理論上的等電點和組成，可以看滴定曲線）?Scratch Protein Predictor?HeliQuest - A web server to scree n seque nces with speci

8、fic alpha-helical properties （ 一個 網站利用專門的alpha螺旋掃描蛋白）?Radar - De novo repeat detect ion in prote in seque nces （蛋白序歹U的重頭重復檢測）?REP - Searches a protein sequenee for repeats （禾U用重復子搜索蛋白）?REPRO - De novo repeat detection in protein seque nces （蛋白序列的重頭重復檢測）?TRUST - De novo repeat detection in protein se

9、que nces （蛋白序列的重頭重復檢測）?XSTREAM - De novo tan dem repeat detect ion and architecture modeli ng in prote in sequences （蛋白序列的串聯重復檢測和體系結構建模）?SAPS - Statistical analysis of protein sequences at EMBnet-CH Also available at EBl （蛋白統計分析）?Coils - Predictio n of coiled coil regi ons in protei ns （Lupass metho

10、d） at EMB net-CH Also available at PBlL（蛋白卷曲螺旋預測）?Paircoil - Prediction of coiled coil regions in proteins （Bergers method）（蛋白的卷曲螺旋預測）?Paircoil2 - Predict ion of the parallel coiled coil fold from seque nee using pairwise residue probabilitis with the Paircoil algorithm.（平行的卷曲螺旋折疊預測）?Multicoil - Pre

11、diction of two- and three-stranded coiled coils（二到三股卷曲螺旋預測）?ePESTfi nd - Ide ntificatio n of PEST regio ns（PEST 區鑒定）?HLA_Bind - Prediction of MHC type I （HLA） peptide binding（ HLA 肽結合預測）?PEPVAC - Prediction of supertypic MHC binders（亞型 MHC 結合者預測）?RANKPEP - Prediction of peptide MHC binding（ MHC 結合預測

12、）?SYFPEITHI - Prediction of MHC type I and II peptide binding（ MH C1 類和 2 類結合預 測）? ProtScale - Amino acid scale representation （Hydrophobicity, other conformational parameters, etc.）（氨基酸標度呈現）?Drawhca - Draw an HCA （Hydrophobic Cluster An alysis） plot of a prote in seque nee（蛋白序列親水性簇分析柱圖的繪制）?Peptide

13、Builder （肽構建）?Prote in Colourer - Tool for colori ng your amino acid seque nee（給氨基酸序歹U上色）?Three To One and One to Three - Tools to con vert a three-letter coded amino acid seque nee to single letter code and vice versa （從3字母密碼子序列到單字母密碼子和反過來）?Three-/on e-letter amino acid con verter - Tool which con

14、verts amino acid codes from three-letter to on e-letter and vice versa.（轉變氨基酸密碼子從3字母到1字母或者相反）?Colorseq - Tool to highlight （i n red） a selected set of residues in a prote in seque nee （標亮 蛋白序列的選定區域）?PepDraw - peptide primary structure draw ing（肽一級結構繪制）?Ra ndSeq - Random prote in seque nee gen erator

15、 （隨機蛋白產生器）?AGADIR - An algorithm to predict the helical content of peptides（肽螺旋量的預測的公式）?APSSP - Adva need Protein Seco ndary Structure Prediction Server（高等的蛋白二級結構預測服務器）?CFSSP - Chou & Fasman Seco ndary Structure Prediction Server（二級結構預測服務器）?GOR - Garnier et al, 1996?HNN - Hierarchical Neural Network

16、 method （Guermeur, 1997）（分層式的神經網絡方法）?HTMSRAP - Helical TransMembrane Segment Rotational Angle Prediction（螺旋跨膜片段旋轉角預測）?Jpred - A consen sus method for prote in sec on dary structure predict ion at Uni versity of Dun dee（蛋白二級結構預測的一致方法）?JUFO - Prote in sec ondary structure predict ion from seque nee （n

17、 eural n etwork）（從序列預測蛋白的二級結構）?NetSurfP - Protein Surface Accessibility and Seco ndary Structure Predictio ns（蛋白表明可進入性和二級結構預測）?NetTur nP - Predict ion of Beta-tur n regions in prote in seque nces（蛋白序歹U的 Beta 轉角預測）?nn Predict - Uni versity of California at San Fran cisco （UCSF） （nn 預測）不能用?Porter - Un

18、i versity College Dublin?PredictProtein - PHDsec, PHDacc, PHDhtm, PHDtopology, PHDthreader, MaxHom, EvalSec from Columbia Uni versity（蛋白預測）?Prof - Cascaded Multiple Classifiers for Secondary Structure Prediction（二級結構預測的級聯的多樣分類）?PSA - BioMolecular Engineering Research Ce nter （BMERC） / Bosto n?PSIpre

19、d - Various protein structure predictio n methods at Bloomsbury Cen tre for Bioin formatics（多樣的蛋白結構預測）?SOPMA - Geourjon and Del eage, 1995?Scratch Protein Predictor?DLP-SVM - Domain linker prediction using SVM at Tokyo University of Agriculture and Technology （域連接預測）?iMolTalk - An In teractive Prote

20、 in Structure An alysis Server （curre ntly dow n）（個相互作用的蛋白結構分析服務器）?MolTalk - A computational environment for structural bioinformatics（結構生物學的計算環境）?COPS - Navigation through fold space and the instantaneous visualization of pairwise structure similarities （）?PoPMuSiC - Predict ion of thermody namic s

21、tability cha nges upon point mutati ons; desig n of modified prote ins?Seq2Struct - A web resource for the ide ntificati on of seque nce-structure links?STRAP - A structural alig nment program for protei ns?TLSMD - TLS （Tra nslatio n/Libratio n/Screw） Motion Determi natio n?TopMatch-web - Protein st

22、ructure comparis on三級結構預測 Tertiary structure predictionHomology modeli ng（同源模型）? SWISS-MODEL - An automated knowledge-based protein modelling server http:/www.expasy.ch/swissmod/SWISS-MODEL.html?CPHmodels - Automated n eural-network based prote in modelli ng server?ESyPred3D - Automated homology mod

23、eli ng program using n eural n etworks?Ge no3d - Automatic modelli ng of protein three-dime nsio nal structureThreadi ng（線頭）?Phyre （Successor of 3D-PSSM） - Automated 3D model building using profile-profile match ing and sec on dary structure?Fugue - Seque nce-structure homology recog niti on?HHpred

24、- Protein homology detect ion and structure predictio n by HMM-HMM comparis on?LOOPP - Seque nee to seque nee, seque nee to structure, and structure to structure alig nment?SAM-T08 - HMM-based Protein Structure Prediction?PSIpred - Various prote in structure predicti on methods （in cludi ng threadi

25、ng） at Bloomsbury Centre for Bioin formaticsAb ini tio（從頭開始）?HMMSTR/Rosetta - Predictio n of protein structure from seque nee評價三級結構預測 Assess ing tertiary structure predictio n?An olea - Atomic Non-Local Environment Assessme nt?LiveBe nch - Continu ous Ben chmark ing of Structure Predictio n Servers?

26、NQ-Flipper - Validati on and correct ion of asparag ine and glutami ne side-cha in amide rotamers in prote in structures solved by X-ray crystallography?PROCHECK - Verificati on of the stereochemical quality of a prote in structure?ProSA-web - Recog niti on of errors in 3D structures of protei ns?QM

27、EAN - Server for Model Quality Estimation?What If - Protein structure analysis program for mutant prediction, structure verification, molecular graphics（四）四級機構 Quaternary structure?MakeMultimer - Rec on structio n of multimeric molecules prese nt in crystals?EBI PISA - Protein In terfaces, Surfaces

28、and Assemblies?PQS - Protein Quaternary Structure Query form at the EBI?ProtBud - Comparis on of asymmetric un its and biological un its from PDB and PQS（五）分子模型和可視化工具Molecular modeli ng and visualizatio n tools?Swiss-PdbViewer - A program to display, an alyse and superimpose prote in 3D structures ?

29、SwissDock- Dock ing of small liga nds into protein active sites with EADock DSS?SwissParam - Topology and parameters for small molecules, for use with CHARMM andGROMAC?Ascalaph Packages?Astex Viewer?Jmol?Marvi nSpace - 3D molecule visualizati on tool?MolMol?MovieMaker - For rapid ren deri ng of prot

30、ein motio ns and in teract ions?PyMol?Rasmol?SRS 3D?VMD?YASARA - Molecular graphics, modeli ng, simulati ons and eLear ning（六）混亂區預測 Predict ion of disordered regions?DisEMBL - Protein disorder predictio n?GlobPlot - Protein disorder/order/globularity/doma in predictor?MeDor - Metaserver or Disorder?

31、POODLE - Prediction Of Order and Disorder by machi ne LEarni ng?List of Protein Disorder Predictors（七）序歹U排歹USeque nee alig nment二元 Binary?SIM + LALNVIEW - Alignment of two protein sequences with SIM, results can be viewed with LALNVIEW?LALIGN - Finds multiple matchi ng subsegme nts in two seque nces

32、?Dotlet - A Java applet for seque nee comparis ons using the dot matrix method多元 Multiple?Decrease redundancy - Reduce a set of sequences into a non-redundant set?Nomad (Neighborhood Optimizati on for Multiple Alig nment Discovery) - Un gapped local multiple alig nment, optimized for prote in seque

33、nces, even whe n dista ntly related?CLUSTALW At EBI, PBIL, My Hits or at EMB net-CH ?KALIGN - An accurate andfast multiple seque nee alig nment algorithm At Karoli nska In stitute or at EBI?MAFFT At Kyushu Un iversity, EBI or at MyHits ?Muscle At Berkeley or at BioAssist?T-Coffee At MyHits , BioAssi

34、st or at EBI?MSA - at Gen estream (IGH)?DIALIGN - Multiple sequenee alignment based on segment-to-segment comparison, at Un iversity of Bielefeld, Germa ny?Match-Box - at Un iversity of Namur, Belgium - at Wash ington Un iversity?Multali n At Geno Toul Bioi nfo or at PBIL?MUSCA - Multiple seque nee

35、alig nment usi ng pattern discovery, at IBM(八) 同源性分析 Alignment analysis?AMAS - An alyse Multiply Alig ned Seque nces?Borks alignment tools - Various tools to enhance the results of multiple alignments (in cludi ng consen sus buildi ng).?CINEMA - Color In teractive Editor for multiple alig nmen ts?ES

36、Pript - Tool to print a multiple alig nment?MaxAlig n - Post-process ing of alig nments by removi ng seque nces (taxa) with many gaps?PhyloGibbs - Gibbs motif sampler in corporat ing phyloge ny and track ing statistics?SVA - Seque nee Variability An alyser for multiple alig nments?PVS - A protein va

37、riability server optimized for con served epitope discovery?WebLogo - Seque nee logos at Berkeley/USA?plogo - Seque nee logos at CBS/De nmark?GENIO/logo - Seque nee logos at Stuttgart/Germa ny?SeqLogo - Seque nee logos at the Immuno medic ine Group, Facultad de Medici na, U.C.M, Spain (The Molecular

38、 Immuno logy Foun dati on (MIF) does not exist anymore)(九) 系統進化分析Phyloge netic an alysis?BIONJ - Server for NJ phyloge netic an alysis?De ndroUPGMA?PHYLIP - Server for phyloge netic an alysis us ing the PHYLIP package?PhyML - Server for ML phyloge netic an alysis?Phyloge ny.fr - Robust Phyloge netic An alysis For The Non-Specialist?The PhylOge netic Web Repeater (POWER) - Performs phyloge netic an alysis?BlastO - Blast on orthologous groups?Evoluti onary Trace Server (T