• CATH

  • Referenced in 3 articles [sw22976]
  • latest version of the CATH-Gene3D protein structure classification database (4.0, http://www.cathdb.info) provides annotations...
  • PFRES

  • Referenced in 6 articles [sw26875]
  • PFRES: protein fold classification by using evolutionary information and predicted secondary structure. MOTIVATION: The number ... tertiary structures. RESULTS: The proposed PFRES method for automated protein fold classification from low identity ... vector and information extracted from the secondary structure predicted with PSI-PRED...
  • SCOP2

  • Referenced in 1 article [sw16875]
  • protein structure mining. We present a prototype of a new structural classification of proteins, SCOP2 ... successor to the Structural Classification of Proteins (SCOP, http://scop.mrc-lmb.cam.ac.uk/scop/) database. Similarly to SCOP ... structure annotation and classification. It defines a new approach to the classification of proteins that ... region of protein structure and sequence. The new classification project is expected to ensure...
  • SOSUI

  • Referenced in 8 articles [sw35979]
  • SOSUI: classification and secondary structure prediction system for membrane proteins. The system SOSUI ... developed, in which the accuracy of the classification of proteins was 99% and the corresponding...
  • Unb-DPC

  • Referenced in 7 articles [sw25079]
  • preserves protein sequence structure information. The experimental results yield SVM based classification accurately...
  • DOMpro

  • Referenced in 4 articles [sw17202]
  • structural and functional units of proteins. The ability to parse protein chains into different domains ... important for protein classification and for understanding protein structure, function, and evolution. Here...
  • PIBASE

  • Referenced in 2 articles [sw29350]
  • pairs of protein domains. It is composed of binary interfaces extracted from structures ... using domain assignments from the Structural Classification of Proteins and CATH fold classification systems. Results ... respectively, based on the topology of secondary structure elements. The utility of the database...
  • SCPRED

  • Referenced in 6 articles [sw26876]
  • sequence. Tests performed with datasets of 1673 protein chains, in which any pair of sequences ... accuracy when predicting the four SCOP-defined structural classes, which is superior when compared with ... Conclusion: The SCPRED can accurately find similar structures for sequences that share low identity with ... features, which are capable of separating the structural classes in spite of their low dimensionality...
  • fastSCOP

  • Referenced in 1 article [sw22474]
  • protein structure. This server uses 3D-BLAST to scan quickly a large structural classification database ... classification accuracy of this server is approximately 98% for 586 query structures and the average ... This server was also evaluated on 8700 structures, which have no annotations in the SCOP ... recognizing the evolutionary classifications and the protein functions of novel structures. The server is accessible...
  • AUTO-MUTE

  • Referenced in 9 articles [sw16878]
  • amino acid replacements. Utilizing cutting-edge supervised classification and regression algorithms, three web-based tools ... upon single residue substitutions in proteins with known native structures. Trained models classify independent mutant...
  • FAUST

  • Referenced in 1 article [sw02343]
  • related proteins. Pairs of functionally related protein structures are searched for sets of chemically equivalent ... maximize classification performance on a training set of irredundant protein structures. The resulting structural template...
  • MemHyb

  • Referenced in 15 articles [sw25194]
  • membrane proteins. Knowledge of membrane protein’s structure and function has great importance in biological ... help in identifying the new membrane protein types based on their primary sequence. In this ... tackle the interesting problem of classifying membrane protein types using their sequence information. We consider ... physicochemical features and provide them to our classification system based on support vector machine...
  • ProCKSI

  • Referenced in 3 articles [sw35361]
  • ProCKSI: a decision support system for Protein (Structure) Comparison, Knowledge, Similarity and Information. Results ... proposed models for given targets where the structures could have a large deviation from ... with the verification of a classification scheme for protein kinases, originally derived by sequence comparison ... consensus similarity measure based on structures. In the third experiment using the Rost and Sander...
  • MAGRE

  • Referenced in 1 article [sw31180]
  • predict regions prone to aggregate in proteins with relative success. We have developed a tool ... order to accomplish classification training, we adopted information of primary structure -- protein sequence -- from...
  • PIRSF

  • Referenced in 1 article [sw22978]
  • relationships of full-length proteins and domains. The primary PIRSF classification unit is the homeomorphic ... structure similarity, domain architecture, functional association, genome context, and phyletic pattern. The results of classification ... protein function and evolution. Domain or fold-based searches allow identification of evolutionarily related protein ... structural folds. Functional convergence and functional divergence are revealed by the relationships between protein classification...
  • SCOPmap

  • Referenced in 2 articles [sw35663]
  • tools applied to a query protein of known structure in order to find the homologs ... classified in SCOP database and thus determine classification assignments. The algorithm is able...
  • PSOFuzzySVM-TMH

  • Referenced in 3 articles [sw27664]
  • owing to the lack of its recognized structures, the identification of TM helix ... exchange group are used to formulate transmembrane protein sequences. The noisy and extraneous attributes ... support vector Machine is utilized as a classification algorithm. Two benchmark datasets, including ... research community for further structure and functional studies on transmembrane proteins...
  • NOXclass

  • Referenced in 3 articles [sw35408]
  • achieve an accuracy of 91.8% for the classification of these three types of interactions using ... allows the interpretation and analysis of protein quaternary structures. In particular, it generates testable hypotheses...
  • FRASS

  • Referenced in 2 articles [sw15707]
  • Gauss integrals and allows one to compare structures of RNA chains and to find similar ... entries in a database derived from the Protein Data Bank. We observed that FRASS scores ... also reproduce satisfactorily the DARTS classification of RNA 3D structures and the classification...
  • LFM-Pro

  • Referenced in 4 articles [sw35378]
  • atoms to detect geometrically significant structural centers of the protein. A feature vector is generated ... family of proteins from a background set of unrelated proteins, and successful features are combined ... into a representative set for the protein family. The utility and success ... serine proteases family of proteins and on a challenging classification dataset via comparison with DALI...