• InterPreTS

  • Referenced in 6 articles [sw35752]
  • InterPreTS: protein Interaction Prediction through Tertiary Structure. Summary: InterPreTS (Interaction Prediction through Tertiary Structure...
  • I-TASSER

  • Referenced in 18 articles [sw17207]
  • protein structure and function prediction based on the sequence-to-structure-to-function paradigm. Starting ... iterative structural assembly simulations. The function of the protein is then inferred by structurally matching ... contains full-length secondary and tertiary structure predictions, and functional annotations on ligand-binding sites ... terms. An estimate of accuracy of the predictions is provided based on the confidence score...
  • TMBpro

  • Referenced in 5 articles [sw11341]
  • contact and tertiary structure prediction of transmembrane β-barrel proteins. Motivation: Transmembrane β-barrel ... mitochondria, Gram-negative bacteria and chloroplasts. These proteins perform critical functions, including active ion-transport ... need for accurate prediction of secondary and tertiary structure of TMB proteins. Traditional homology modeling...
  • PFRES

  • Referenced in 6 articles [sw26875]
  • evolutionary information and predicted secondary structure. MOTIVATION: The number of protein families has been estimated ... slowing down. This indicates that the protein structure space will be soon covered and thus ... Present tertiary structure prediction methods behave well when a homologous structure is predicted, but give ... prediction of tertiary structures. RESULTS: The proposed PFRES method for automated protein fold classification from...
  • DCMOGADES

  • Referenced in 2 articles [sw02761]
  • problems, adjustment problems of control, prediction of protein tertiary structure problems...
  • DeepQA

  • Referenced in 1 article [sw15927]
  • major challenges for protein tertiary structure prediction. Especially, estimating the quality of a single protein...
  • CONFOLD

  • Referenced in 1 article [sw17008]
  • methods are available to construct protein tertiary structures from predicted contacts. Here, we present ... using predicted contacts and secondary structures. Our method first translates contacts and secondary structures into ... distance geometry algorithm to build tertiary structure models. The initially reconstructed models are used ... contacts and secondary structures improves the quality and accuracy of structural models and in particular...
  • NETASA

  • Referenced in 3 articles [sw35774]
  • solvent accessibility. Motivation: Prediction of the tertiary structure of a protein from its amino acid ... important problems in molecular biology. The successful prediction of solvent accessibility will be very helpful...
  • ExPASy

  • Referenced in 14 articles [sw34228]
  • databases and analytical tools dedicated to proteins and proteomics. ExPASy databases include SWISS-PROT ... post-translational modification prediction, topology prediction, primary, secondary and tertiary structure analysis and sequence alignment...
  • DNdisorder

  • Referenced in 2 articles [sw16907]
  • number of proteins contain regions which do not adopt a stable tertiary structure in their ... sequence based approach for the prediction of protein disorder. The method uses boosted ensembles...
  • MAMMOTH

  • Referenced in 11 articles [sw26215]
  • Advances in structural genomics and protein structure prediction require the design of automatic, fast, objective ... structures, via experimental or theoretical approaches. Here, a new method for sequence-independent structural alignment ... experimental protein structure with an arbitrary low-resolution protein tertiary model. The heuristic algorithm...
  • PREvaIL

  • Referenced in 10 articles [sw25073]
  • understanding the relationship between protein sequence, structure, function, and enhancing our ability to design novel ... been sequenced, and their primary and tertiary structures determined, experimental methods for enzyme functional characterization ... modern sequence- and structure-based methods, showed that PREvaIL achieved competitive predictive performance, with ... both understanding the complex sequence-structure-function relationships of proteins and facilitating the characterization...
  • MULTICOM

  • Referenced in 2 articles [sw15827]
  • tertiary structures determined by experimental techniques. And the gap between protein sequence and structure will ... much higher than protein structure determination techniques. Computational tools of predicting the structure and structural...
  • Matlab

  • Referenced in 12309 articles [sw00558]
  • MATLAB® is a high-level language and interactive...
  • R

  • Referenced in 8601 articles [sw00771]
  • R is a language and environment for statistical...
  • STAR

  • Referenced in 12 articles [sw02515]
  • STAR: ultrafast universal RNA-seq aligner. Motivation: Accurate...
  • Bioconductor

  • Referenced in 305 articles [sw04205]
  • Bioconductor provides tools for the analysis and comprehension...
  • Rfam

  • Referenced in 33 articles [sw04637]
  • The Rfam database is a collection of RNA...
  • alphaBB

  • Referenced in 49 articles [sw06249]
  • alphaBB: A Global Optimization Method for General Constrained...
  • ode23

  • Referenced in 285 articles [sw06600]
  • The MATLAB ODE Suite: ode23: Solve nonstiff differential...