• ViennaRNA

  • Referenced in 20 articles [sw10504]
  • comparison of RNA secondary structures. RNA secondary structure prediction through energy minimization is the most ... kinds of dynamic programming algorithms for structure prediction: the minimum free energy algorithm of (Zuker ... Stiegler 1981) which yields a single optimal structure, the partition function algorithm of (McCaskill ... suboptimal structures within a given energy range of the optimal energy. For secondary structure comparison...
  • Pfold

  • Referenced in 12 articles [sw23813]
  • Hein, J. J.: Pfold: RNA secondary structure prediction using stochastic context-free grammars ... secondary structures are important in many biological processes and efficient structure prediction can give vital ... investigations. Many available programs for RNA secondary structure prediction only use a single sequence ... presents a practical way of predicting RNA secondary structure that is especially useful when related...
  • Mfold

  • Referenced in 41 articles [sw12672]
  • Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids...
  • PSIPRED

  • Referenced in 14 articles [sw11340]
  • protein structure prediction server allows users to submit a protein sequence, perform a prediction ... choice and receive the results of the prediction both textually via e-mail and graphically ... their sequence: PSIPRED, a highly accurate secondary structure prediction method; MEMSAT 2, a new version...
  • CONTRAfold

  • Referenced in 8 articles [sw17117]
  • dominant strategy for single sequence RNA secondary structure prediction. More recently, stochastic context-free grammars ... alternative probabilistic methodology for modeling RNA structure. Unlike physics-based methods, which rely on thousands ... based models. CONTRAfold is a novel secondary structure prediction method based on conditional log-linear ... measurement of thermodynamic parameters for RNA secondary structure prediction...
  • JPred

  • Referenced in 7 articles [sw35977]
  • JPred: a consensus secondary structure prediction server. An interactive protein secondary structure prediction Internet server ... submitted, and returns predictions from six secondary structure prediction algorithms that exploit evolutionary information from...
  • Lynx

  • Referenced in 10 articles [sw13643]
  • from computational biology, namely, the RNA secondary structure prediction problem. The constraints that make...
  • RNAsoft

  • Referenced in 7 articles [sw09073]
  • RNAsoft: a suite of RNA secondary structure prediction and design software tools ... tools for prediction and design of molecular structure will be needed in these applications ... programs provides tools for predicting the secondary structure of a pair...
  • PFRES

  • Referenced in 6 articles [sw26875]
  • classification by using evolutionary information and predicted secondary structure. MOTIVATION: The number of protein families ... that the growth in discovery of novel structures that are deposited into ... remaining structures by using the known folding patterns. Present tertiary structure prediction methods behave well ... vector and information extracted from the secondary structure predicted with PSI-PRED...
  • SCPRED

  • Referenced in 6 articles [sw26876]
  • features as its input to predict the structural classes. Based on extensive design that considers ... along with features based on the predicted secondary structure and content, the classifier’s input ... based on information extracted from the secondary structure predicted with PSI-PRED and one feature...
  • 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 ... server run contains full-length secondary and tertiary structure predictions, and functional annotations on ligand...
  • SOSUI

  • Referenced in 8 articles [sw35979]
  • SOSUI: classification and secondary structure prediction system for membrane proteins. The system SOSUI...
  • UNAFold

  • Referenced in 8 articles [sw12671]
  • from “Unified Nucleic Acid Folding.” Folding (secondary structure) prediction for single-stranded ... including Mac OS X. Images of secondary structures, hybridizations, and dot plots may be computed...
  • RNAstructure

  • Referenced in 3 articles [sw17133]
  • RNAstructure: software for RNA secondary structure prediction and analysis. Background: To understand an RNA sequence ... RNAs and antisense DNA oligonucleotides. RNA secondary structure prediction, using thermodynamics, can be used ... software package for RNA secondary structure prediction and analysis. It uses thermodynamics and utilizes ... Turner group. It includes methods for secondary structure prediction (using several algorithms), prediction of base...
  • Porter

  • Referenced in 4 articles [sw16910]
  • accurate server for protein secondary structure prediction. Summary: Porter is a new system for protein ... secondary structure prediction in three classes. Porter relies on bidirectional recurrent neural networks with shortcut...
  • PSNO

  • Referenced in 6 articles [sw27678]
  • features, including the evolutionary profile, the predicted secondary structure and the physicochemical properties. Secondly, rather ... selection scheme, our method, PSNO, achieves good prediction performance with a mean Mathews correlation coefficient...
  • PROMALS

  • Referenced in 4 articles [sw22476]
  • essential in homology inference, structure modeling, functional prediction and phylogenetic analysis. We developed ... homologs from PSI-BLAST searches and secondary structure predictions from PSIPRED. PROMALS shows higher alignment ... augmented with information about sequence grouping, predicted secondary structures and positional conservation. The PROMALS...
  • Sfold

  • Referenced in 13 articles [sw23820]
  • statistical sampling paradigm for the prediction of RNA secondary structure. One of the main objectives ... combination of RNA target accessibility prediction, siRNA duplex thermodynamic properties and empirical design rules...
  • FORESST

  • Referenced in 3 articles [sw26866]
  • FORESST: fold recognition from secondary structure predictions of proteins. MOTIVATION: A method for recognizing ... hidden Markov models (HMMs) and secondary structure prediction was recently developed for proteins ... this approach is novel in that only secondary structure information is used. Each ... proteins having a similar fold. Secondary structure prediction is performed for the amino acid sequence...
  • NNDB

  • Referenced in 7 articles [sw23805]
  • neighbor parameter database for predicting stability of nucleic acid secondary structure. The Nearest Neighbor Database ... disseminating parameter sets for predicting nucleic acid secondary structure stabilities. For each set of parameters ... tutorials. The initial release covers parameters for predicting RNA folding free energy and enthalpy changes...