• SCPRED

  • Referenced in 6 articles [sw26876]
  • SCPRED: Accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting ... protein or its domain is defined as the structural class. Current structural class prediction methods ... input to predict the structural classes. Based on extensive design that considers over 2300 index ... when predicting the four SCOP-defined structural classes, which is superior when compared with over...
  • PreSSAPro

  • Referenced in 2 articles [sw00730]
  • homogeneous data sets corresponding to protein structural classes, i.e., all-alpha, all-beta, or alpha ... evaluated for the right protein class. PreSSAPro predicts the secondary structure according to the right ... protein class, if known, or gives a multiple prediction with reference to the different structural ... depending on the structural class assignment, in the perspective of identifying proteins able to fold...
  • FORESST

  • Referenced in 3 articles [sw26866]
  • structural class. Here, this methodology is extended to Mainly-Beta and Alpha-Beta class proteins ... approach is novel in that only secondary structure information is used. Each HMM is trained ... rate on 44 test proteins covering the three structural classes was found ... performed prior to the publication of experimental structure, the success rate was 71%. In conclusion...
  • Porter

  • Referenced in 4 articles [sw16910]
  • system for protein secondary structure prediction in three classes. Porter relies on bidirectional recurrent neural ... cross-validation on a large set of proteins, exceeds 79%, significantly above a copy...
  • BALL

  • Referenced in 5 articles [sw10727]
  • classes for Molecular Mechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export...
  • PROFEAT

  • Referenced in 14 articles [sw16924]
  • composition, transition and distribution of various structural and physicochemical properties. In addition, it can also ... protein features have been used in a number of published works for predicting proteins ... functional classes, proteinprotein interactions and MHC-binding peptides. PROFEAT is accessible at http://jing.cz3.nus.edu.sg...
  • StrBioLib

  • Referenced in 2 articles [sw16906]
  • biology research. StrBioLib contains classes to represent and manipulate protein structures, biopolymer sequences, sets...
  • MAGRE

  • Referenced in 1 article [sw31180]
  • predictor categories according to protein structural information: General and Folding Class. We have selected ... class in order to develop the predictor. We conducted testing with randomly selected protein sequences...
  • MBT

  • Referenced in 1 article [sw10735]
  • toolkit provides classes for efficiently loading, managing and manipulating protein structure and sequence data ... toolkit, the core data i/o and manipulation classes may be used to write completely...
  • PredLactamase

  • Referenced in 12 articles [sw16470]
  • primary structures, β-lactamase family of enzymes is divided into four classes namely ... Class B are metallo-enzymes while A, C and D does not need any metal ... based two level β-lactamases protein prediction method, which differentiate β-lactamases from...
  • Fu-SulfPred

  • Referenced in 3 articles [sw36890]
  • identifying protein S-sulfenylation sites can be influenced by a class imbalance of training datasets ... stratified structure of three kinds of decision trees in order to identify possible protein...
  • Intersurf

  • Referenced in 2 articles [sw32934]
  • understand the process thanks to 3D protein structures, to estimate the quality of docking simulation ... order to predict docking affinity between classes of interacting zones. Since the interface ... surface that separates the two proteins, it is possible to create a map of interaction...
  • PROFcon

  • Referenced in 5 articles [sw35542]
  • information from alignments, from predictions of secondary structure and solvent accessibility, from the region between ... entire protein. In contrast to some other methods, PROFcon predicted short and long proteins ... accuracy was highest for proteins belonging to the SCOP alpha/beta class. PROFcon compared favorably with ... seed predictions of global features of protein structure. Availability:http://www.predictprotein.org/submit_profcon.html...
  • PRED-CLASS

  • Referenced in 5 articles [sw26873]
  • proteins (success rate approximately 96%) unambiguously assigned into one of the target classes. The application ... PRED-CLASS to several test sets and complete proteomes of several organisms demonstrates that such ... step in fold recognition and ab initio structure prediction methods. Detailed results obtained for various...
  • mmLib

  • Referenced in 4 articles [sw04609]
  • elements and monomers, an object-oriented data structure describing biological macromolecules, and an OpenGL molecular ... modeling, and visualization. This includes specialized classes for proteins, DNA, amino acids, and nucleic acids...
  • ConsDock

  • Referenced in 1 article [sw09660]
  • very good accuracy for both the protein-bound orientation and the conformation of the ligand ... consensus pairs into classes, represented by a mean structure; and (iv) ranking the different means ... populated class of consensus pairs. When applied to a test set of 100 protein-ligand ... complexes from the Protein Data Bank, ConsDock significantly outperforms single docking with respect...
  • VR-BFDT

  • Referenced in 1 article [sw22448]
  • machine learning domain in which a protein (regarded as instance) may have more than ... regarded as classes) are dependent and also are organized in a hierarchical structure ... proposed to predict functions of the proteins. This algorithm just fuzzifies the decision boundaries instead ... each protein simultaneously and preserves the hierarchy consistency between functional classes. It uses the label...
  • PIBASE

  • Referenced in 2 articles [sw29350]
  • using domain assignments from the Structural Classification of Proteins and CATH fold classification systems. Results ... complexes are grouped into 989 topological classes based on their patterns of domain–domain contacts ... topological classes, respectively, based on the topology of secondary structure elements. The utility...
  • ProtorP

  • Referenced in 2 articles [sw35300]
  • structure contributions. The server is flexible, in that it allows users to analyse individual protein ... distributions for non-homologous datasets of different classes of protein associations provided on the server...
  • CCMpred

  • Referenced in 1 article [sw17014]
  • made reliable de novo prediction of protein structures possible. The key was to apply statistical ... separate direct from indirect effects. Two classes of such methods exist, either relying on regularized ... large-scale contact prediction for larger protein families, multi-domain proteins and proteinprotein interactions...