• clue

  • Referenced in 14 articles [sw09497]
  • creating and analyzing cluster ensembles, with basic data structures for representing partitions and hierarchies...
  • ProDy

  • Referenced in 4 articles [sw24072]
  • theoretically predicted equilibrium dynamics. Datasets include structural ensembles for a given family or subfamily...
  • ViennaRNA

  • Referenced in 22 articles [sw10504]
  • Stiegler 1981) which yields a single optimal structure, the partition function algorithm of (McCaskill ... ensemble, and the suboptimal folding algorithm of (Wuchty et.al 1999) which generates all suboptimal structures...
  • PROMOTIF

  • Referenced in 5 articles [sw26864]
  • related structures, such as an ensemble of NMR structures...
  • RNAfold

  • Referenced in 5 articles [sw10505]
  • structure and prints to stdout the mfe structure in bracket notation and its free energy ... prints the free energy of the thermodynamic ensemble ... frequency of the mfe structure in the ensemble, and the ensemble diversity to stdout...
  • Chimera

  • Referenced in 34 articles [sw10908]
  • interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies ... sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations...
  • OpenRec

  • Referenced in 3 articles [sw29798]
  • computational graph that consists of a structured ensemble of reusable modules connected through...
  • RNACluster

  • Referenced in 2 articles [sw23124]
  • house structure matrix distance, and one effective cluster approach for the ensemble clustering using ... study the characteristics of RNA secondary structures, RNA structure conformational switches, RNA conformational energy landscapes ... prediction based on the clustering of structure ensemble...
  • MAVEN

  • Referenced in 2 articles [sw35124]
  • visualization of elastic networks and structural ensembles. Results: Our new software, MAVEN, aims to bring...
  • horserule

  • Referenced in 4 articles [sw27913]
  • package horserule: Tree ensembles with rule structured horseshoe regularization. We propose a new Bayesian model ... flexible nonlinear regression and classification using tree ensembles. The model is based on the RuleFit...
  • RNAG

  • Referenced in 2 articles [sw17129]
  • that the RNAG sampled structures were generally compact around their ensemble centroids, and at least ... least two well-separated clusters of predicted structures. In general, the distance between a reference ... relative to the variation among structures within an ensemble. Availability: The Perl implementation...
  • CARNA

  • Referenced in 1 article [sw23122]
  • sequences based on their full ensembles of structures. Alternatively, you can also provide base pair ... structures and not the entire ensemble of possible structures is aligned. In contrast to LocARNA...
  • RNAKinetics

  • Referenced in 4 articles [sw23818]
  • software models the dynamics of RNA secondary structure by the means of kinetic analysis ... modeling is a kinetic ensemble, i.e. a collection of RNA structures that are endowed with...
  • GeneWise

  • Referenced in 5 articles [sw29729]
  • defined spliced structure. Both algorithms are heavily used by the Ensembl annotation system. The GeneWise ... provide both accurate and complete gene structures when used with the correct evidence...
  • SCPRED

  • Referenced in 6 articles [sw26876]
  • accuracy when predicting the four SCOP-defined structural classes, which is superior when compared with ... ensemble of classifiers predictors. Conclusion: The SCPRED can accurately find similar structures for sequences that...
  • Osprey

  • Referenced in 3 articles [sw21400]
  • proteins and ligands as ensembles of low-energy structures to better approximate binding affinity ... resistance mutations and explain why improved flexibility, ensembles, and provability are essential for this application...
  • QuatIdent

  • Referenced in 6 articles [sw22479]
  • quaternary structural attributes in a timely manner. In view of this, a powerful ensemble identifier ... following 10 main quaternary structural attributes: (1) monomer, (2) dimer, (3) trimer, (4) tetramer...
  • GenomeGraphs

  • Referenced in 4 articles [sw17313]
  • annotation queries to Ensembl and translates this to e.g. gene/transcript structures in viewports...
  • FoldRate

  • Referenced in 15 articles [sw35301]
  • knowledge of their 3D (three dimensional) structures is becoming increasingly wide. It is highly desired ... information alone. To address this problem, an ensemble predictor, called FoldRate, was developed by fusing ... however, need both the sequence and 3D structure information for predicting the folding rate...
  • RactIP

  • Referenced in 2 articles [sw17120]
  • been devoted to predicting joint secondary structures or binding sites under a specific class ... integrate approximate information on an ensemble of equilibrium joint structures into the objective function...