• PFRES

  • Referenced in 6 articles [sw26875]
  • classification by using evolutionary information and predicted secondary structure. MOTIVATION: The number of protein families ... known folding patterns. Present tertiary structure prediction methods behave well when a homologous structure ... similarity would be beneficial for prediction of tertiary structures. RESULTS: The proposed PFRES method ... information extracted from the secondary structure predicted with PSI-PRED...
  • Lynx

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

  • Referenced in 7 articles [sw17377]
  • essential component of protein structure prediction, since ultimately the accuracy of a model determines ... Usually, in the course of protein structure prediction a set of alternative models is produced...
  • PseAAC-General

  • Referenced in 16 articles [sw22430]
  • used to represent protein sequences in predicting protein structural and functional attributes. We developed...
  • NNcon

  • Referenced in 6 articles [sw17013]
  • rate prediction, model selection and 3D structure prediction. Here we describe NNcon, a fast ... reliable contact map prediction server and software. NNcon was ranked among the most accurate residue ... Critical Assessment of Techniques for Protein Structure Prediction (CASP8), 2008. Both NNcon server and software...
  • RNAsoft

  • Referenced in 7 articles [sw09073]
  • RNAsoft: a suite of RNA secondary structure prediction and design software tools ... software 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...
  • RNAstructure

  • Referenced in 4 articles [sw17133]
  • RNAstructure: software for RNA secondary structure prediction and analysis. Background: To understand an RNA sequence ... antisense DNA oligonucleotides. RNA secondary structure prediction, using thermodynamics, can be used to develop hypotheses ... software package for RNA secondary structure prediction and analysis. It uses thermodynamics and utilizes ... group. It includes methods for secondary structure prediction (using several algorithms), prediction of base pair...
  • MaxSub

  • Referenced in 8 articles [sw35908]
  • measure for the assessment of protein structure prediction quality. Results: MaxSub ... model that superimpose ‘well’ over the experimental structure, and produces a single normalized score that ... evaluation method for assessment measures of predicted models, it is not easy to evaluate...
  • FoldRate

  • Referenced in 15 articles [sw35301]
  • FoldRate: A Web-Server for Predicting Protein Folding Rates from Primary Sequence. With the avalanche ... knowledge of their 3D (three dimensional) structures is becoming increasingly wide. It is highly desired ... velop a method by which one can predict the folding rates of proteins based ... both the sequence and 3D structure information for predicting the folding rate. As a user...
  • KineFold

  • Referenced in 8 articles [sw33134]
  • server for RNA/DNA folding path and structure prediction including pseudoknots and knots...
  • SOSUI

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

  • Referenced in 5 articles [sw22442]
  • sequence using random forest method. Prediction of protein structure from its amino acid sequence ... folding is essential for the accurate structure prediction. Knowledge of residue solvent accessibility gives useful ... insights into protein structure prediction and function prediction. In this work, we propose a random ... useful for prediction of residue solvent accessibility from protein sequence without using structural information...
  • UNAFold

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

  • Referenced in 43 articles [sw04319]
  • Java, and Perl programs, and in record-structured data sources; it is easy to extend ... cases, predicting incompatibilities in component integration, automating theorem proving, repairing inconsistent data structures, and checking...
  • PSICOV

  • Referenced in 5 articles [sw17010]
  • PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments ... Motivation: The accurate prediction of residue–residue contacts, critical for maintaining the native fold ... have major impacts in both structure and function prediction to name but two benefits. Sequence ... significant benefit in protein structure prediction or model quality assessment. Availability: The PSICOV source code...
  • pystruct

  • Referenced in 4 articles [sw14411]
  • Pystruct-learning structured prediction in Python. Structured prediction methods have become a central tool ... general purpose implementation of standard structured prediction methods, both for practitioners and as a baseline...
  • HHpred

  • Referenced in 7 articles [sw17271]
  • remote protein homology detection and structure prediction and is the first to implement pairwise comparison ... local or global alignment and scoring secondary structure similarity. HHpred can produce pairwise query-template...
  • ESyPred3D

  • Referenced in 5 articles [sw16876]
  • ESyPred3D: Prediction of proteins 3D structures. Motivation: Homology or comparative modeling is currently the most ... accurate method to predict the three-dimensional structure of proteins. It generally consists in four ... Critical Assessment of Techniques for Proteins Structural Prediction). Our alignment strategy obtains better results compared...
  • DOMpro

  • Referenced in 4 articles [sw17202]
  • DOMpro: Protein domain prediction using profiles, secondary structure, relative solvent accessibility, and recursive neural networks ... protein classification and for understanding protein structure, function, and evolution. Here we use machine learning ... information in the form of profiles, predicted secondary structure, and predicted relative solvent accessibility. DOMpro ... Critical Assessment of Fully Automated Structure Prediction 4 (CAFASP-4) (Fisher et al., 1999; Saini...
  • GlobPlot

  • Referenced in 8 articles [sw06213]
  • structural genomics era is to predict protein structure and function, including identification of those proteins...