CATH: increased structural coverage of functional space.
CATH: increased structural coverage of functional space.
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DOI：
10.1093/nar/gkaa1079
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发表时间：
2021-01-08
影响因子：
14.9
通讯作者：
Orengo CA
中科院分区：
文献类型：
--
作者：
Sillitoe I;Bordin N;Dawson N;Waman VP;Ashford P;Scholes HM;Pang CSM;Woodridge L;Rauer C;Sen N;Abbasian M;Le Cornu S;Lam SD;Berka K;Varekova IH;Svobodova R;Lees J;Orengo CA
CATH（https://www.cathdb.info）识别来自WWPDB的蛋白质结构中的结构域，并将其分类为进化的超家族，从而提供结构和功能注释。有两个级别：CATH-B，最新域结构和超家族分配的每日快照，以及带有其他派生数据的CATH+，例如预测的序列域，以及功能相干序列子集（功能家族或Funfams）。最新的CATA+版本4.3显着增加了结构和序列数据的覆盖范围，并增加了65,351个完全分类的域结构（+15％），提供了500 238个结构域，1.51亿个预测的序列域（+59％）分配给5481个超家族。 Funfam生成管道已经过重新设计，以应对数据涌入的增加。在Funfams中捕获了三倍的序列，其功能纯度，信息含量和结构覆盖范围也随之增加。 Funfam扩展增加了为实验GO项提供的结构注释（+59％）。我们还提出了Cath-Funvar网页，以显示蛋白质序列的变化及其与已知或预测的功能部位的近端。我们提出了两项案例研究（1）假定的癌症驱动因素和（2）SARS-COV-2蛋白。最后，我们改善了与SCOP，InterPro，Aquaria和2Dprot在内的CATA的链接。
CATH (https://www.cathdb.info) identifies domains in protein structures from wwPDB and classifies these into evolutionary superfamilies, thereby providing structural and functional annotations. There are two levels: CATH-B, a daily snapshot of the latest domain structures and superfamily assignments, and CATH+, with additional derived data, such as predicted sequence domains, and functionally coherent sequence subsets (Functional Families or FunFams). The latest CATH+ release, version 4.3, significantly increases coverage of structural and sequence data, with an addition of 65,351 fully-classified domains structures (+15%), providing 500 238 structural domains, and 151 million predicted sequence domains (+59%) assigned to 5481 superfamilies. The FunFam generation pipeline has been re-engineered to cope with the increased influx of data. Three times more sequences are captured in FunFams, with a concomitant increase in functional purity, information content and structural coverage. FunFam expansion increases the structural annotations provided for experimental GO terms (+59%). We also present CATH-FunVar web-pages displaying variations in protein sequences and their proximity to known or predicted functional sites. We present two case studies (1) putative cancer drivers and (2) SARS-CoV-2 proteins. Finally, we have improved links to and from CATH including SCOP, InterPro, Aquaria and 2DProt.
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影响因子：
14.9
作者：
Sillitoe I;Dawson N;Lewis TE;Das S;Lees JG;Ashford P;Tolulope A;Scholes HM;Senatorov I;Bujan A;Ceballos Rodriguez-Conde F;Dowling B;Thornton J;Orengo CA
通讯作者：
Orengo CA
影响因子：
--
作者：
Patani H;Bunney TD;Thiyagarajan N;Norman RA;Ogg D;Breed J;Ashford P;Potterton A;Edwards M;Williams SV;Thomson GS;Pang CS;Knowles MA;Breeze AL;Orengo C;Phillips C;Katan M
通讯作者：
Katan M
影响因子：
14.9
作者：
Mistry J;Finn RD;Eddy SR;Bateman A;Punta M
通讯作者：
Punta M
DOI：
10.1093/bioinformatics/bty863
发表时间：
2019-05-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Lewis TE;Sillitoe I;Lees JG
通讯作者：
Lees JG
影响因子：
12.3
作者：
Jiang Y;Oron TR;Clark WT;Bankapur AR;D'Andrea D;Lepore R;Funk CS;Kahanda I;Verspoor KM;Ben-Hur A;Koo da CE;Penfold-Brown D;Shasha D;Youngs N;Bonneau R;Lin A;Sahraeian SM;Martelli PL;Profiti G;Casadio R;Cao R;Zhong Z;Cheng J;Altenhoff A;Skunca N;Dessimoz C;Dogan T;Hakala K;Kaewphan S;Mehryary F;Salakoski T;Ginter F;Fang H;Smithers B;Oates M;Gough J;Törönen P;Koskinen P;Holm L;Chen CT;Hsu WL;Bryson K;Cozzetto D;Minneci F;Jones DT;Chapman S;Bkc D;Khan IK;Kihara D;Ofer D;Rappoport N;Stern A;Cibrian-Uhalte E;Denny P;Foulger RE;Hieta R;Legge D;Lovering RC;Magrane M;Melidoni AN;Mutowo-Meullenet P;Pichler K;Shypitsyna A;Li B;Zakeri P;ElShal S;Tranchevent LC;Das S;Dawson NL;Lee D;Lees JG;Sillitoe I;Bhat P;Nepusz T;Romero AE;Sasidharan R;Yang H;Paccanaro A;Gillis J;Sedeño-Cortés AE;Pavlidis P;Feng S;Cejuela JM;Goldberg T;Hamp T;Richter L;Salamov A;Gabaldon T;Marcet-Houben M;Supek F;Gong Q;Ning W;Zhou Y;Tian W;Falda M;Fontana P;Lavezzo E;Toppo S;Ferrari C;Giollo M;Piovesan D;Tosatto SC;Del Pozo A;Fernández JM;Maietta P;Valencia A;Tress ML;Benso A;Di Carlo S;Politano G;Savino A;Rehman HU;Re M;Mesiti M;Valentini G;Bargsten JW;van Dijk AD;Gemovic B;Glisic S;Perovic V;Veljkovic V;Veljkovic N;Almeida-E-Silva DC;Vencio RZ;Sharan M;Vogel J;Kansakar L;Zhang S;Vucetic S;Wang Z;Sternberg MJ;Wass MN;Huntley RP;Martin MJ;O'Donovan C;Robinson PN;Moreau Y;Tramontano A;Babbitt PC;Brenner SE;Linial M;Orengo CA;Rost B;Greene CS;Mooney SD;Friedberg I;Radivojac P
通讯作者：
Radivojac P