一、蛋白质结构分类数据库：

SCOP2 is a successor of Structural classification of proteins(SCOP)    

【http://scop2.mrc-lmb.cam.ac.uk/】

CATH is a classification of protein structures downloaded from the Protein Data Bank

【http://www.cathdb.info/】

二、常用的蛋白质结构比对方法

1. 策略：CE

策略要点：分子内距离比较方法，采用最优路径扩张的策略

【http://cl.sdsc.edu/jfatcatserver/】

2. 策略：TM-align

策略要点：类似于分子内距离比较方法动态规划

【http://zhanglab.ccmb.med.umich.edu/TM-align/】

简介：TM-align is an algorithm for sequence-order independent protein structure comparisons. For two protein structures of unknown equivalence, TM-align first generates optimized residue-to-residue alignment based on structural similarity using dynamic programming iterations. An optimal superposition of the two structures, as well as the TM-score value which scales the structural similarity, will be returned. TM-score has the value in (0,1], where 1 indicates a perfect match between two structures. Following strict statistics of structures in the PDB, scores below 0.2 corresponds to randomly chosen unrelated proteins whereas with a score higher than 0.5 assume generally the same fold in SCOP/CATH.

3. 策略：DAL1

策略要点：分子内距离比较方法

【http://www.ebi.ac.uk/Tools/structure/dalilite/】

简介：DaliLite computes optimal and suboptimal structural alignments between two protein structures. It will compare all chains in the first structure against all chains in the second (unless specific chain IDs are given). The resulting superimposed coordinate files can be downloaded or viewed interactively in Jmol.

4. 策略：K2

策略要点：遗传算法

【http://zlab.bu.edu/k2sa/index.shtml】

简介：K2SA is a protein structure alignment program based on K2. K2SA uses the same basic strategy as K2 but is about 100 times faster. This speed up is the result of

1) A fast simulated annealing technique that replaces the genetic algorithm.

2) Tighter code.

5. 策略：SHEBA

策略要点：分层次比对

【https://ccrod.cancer.gov/confluence/display/CCRLEE/SHEBA】

简介：SHEBA is a new protein structure alignment procedure. The initial alignment is made by comparing a one-dimensional (1D) list of primary, secondary and tertiary structural profiles of two proteins, without explicitly considering the geometry of the structures. The alignment is then iteratively refined in the second step, in which new alignments are found by three-dimensional (3D) superposition of the structures based on the current alignment.

SHEBA can do pair-wise (one-to-one) alignment or multiple (one-to-many) alignment. It also has several different output options:

1) for pair-wise alignment: alignment statistics, corresponding sequence alignments, formatted column output, a list of aligned residue numbers, the transformation matrix, and the transformed coordinates in PDB-like format.

2) for multiple alignment: corresponding sequence alignments and multiple alignment statistics.

6. 策略：MultiProt

策略要点：多结构比对方法

【http://bioinfo3d.cs.tau.ac.il/MultiProt/】

简介：MultiProt is a fully automated highly efficient technique which detects the multiple structural alignments of protein structures. It finds the common geometrical cores between the input molecules. Most of the existing methods require that all the input molecules be aligned, while MultiProt does not require that all the input molecules participate in the alignment. Actually, it efficiently detects high scoring partial multiple alignments for all possible number of molecules from the input.

The final structural alignment can either preserve the sequence order (like sequence alignment), or be sequence order independent.

7. 策略：SSM

策略要点：基于二级结构单元匹配

【http://www.ebi.ac.uk/msd-srv/ssm/】

简介：

PDBeFold functionality:

1) pairwise comparison and 3D alignment of protein structures

2) multiple comparison and 3D alignment of protein structures

3) examination of a protein structure for similarity with the whole PDB archive or SCOP archive

4) best Cα-alignment of compared structures

5) download and visualisation of best-superposed structures using Rasmol (Unix/Linux platforms),Rastop (Windows machines) and Jmol (platform-independent server-side java viewer)

6) linking the results to other services -PDBeMotif,SCOP,GeneCensus,FSSP,CATH,PDBSum,UniProt

8. 策略：STRUCTURAL

策略要点：基于双动态规划

【http://molmovdb.mbb.yale.edu/align/】

简介：Structural Alignment Server

9. 策略：VAST

策略要点：基于图论的方法

【http://www.ncbi.nlm.nih.gov/Structure/VAST/vastsearch.html】

简介：Vector Alignment Search Tool

VAST, short for Vector Alignment Search Tool, is a computer algorithm developed at NCBI and used to identify similar protein 3-dimensional structures ("similar structures") by purely geometric criteria, and to identify distant homologs that cannot be recognized by sequence comparison.

10. 策略：SuperPose

策略要点：基于四元数特征值算法比对

【http://wishart.biology.ualberta.ca/SuperPose/】

简介：SuperPose is a protein superposition server. SuperPose calculates protein superpositions using a modified quaternion approach. From a superposition of two or more structures, SuperPose generates sequence alignments, structure alignments, PDB coordinates, RMSD statistics, Difference Distance Plots, and interactive images of the superimposed structures.  The SuperPose web server supports the submission of either PDB-formatted files or PDB accession numbers.

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