• FoldRate

  • Referenced in 15 articles [sw35301]
  • FoldRate: A Web-Server for Predicting Protein Folding Rates from Primary Sequence. With the avalanche ... postgenomic age, the gap between newly found protein sequences and the knowledge of their ... which one can predict the folding rates of proteins based on their amino acid sequence ... called FoldRate, was developed by fusing the folding-correlated features that can be either directly...
  • MCAMC

  • Referenced in 12 articles [sw02829]
  • Carlo simulations from magnetization switching to protein folding We present the Monte Carlo with Absorbing ... some of the characteristics of protein folding and could also be experimentally realizable in domain...
  • PFRES

  • Referenced in 6 articles [sw26875]
  • PFRES: protein fold classification by using evolutionary information and predicted secondary structure. MOTIVATION: The number ... slowing down. This indicates that the protein structure space will be soon covered and thus ... time, some proteins that share twilight-zone sequence identity can form similar folds. Therefore, determination ... proposed PFRES method for automated protein fold classification from low identity (<35%) sequences obtains...
  • iHSP-PseRAAAC

  • Referenced in 16 articles [sw25193]
  • play essential roles in protein-protein interactions such as folding and assisting in the establishment...
  • KineticDB

  • Referenced in 3 articles [sw16246]
  • KineticDB: a database of protein folding kinetics. We propose here KineticDB, a systematically compiled database ... protein folding kinetics, which contains about 90 unique proteins. The main goal of the KineticDB ... users with a diverse set of protein folding rates determined experimentally. The search for determinants ... protein folding is still in progress, aimed at obtaining a new understanding of the folding...
  • TM-align

  • Referenced in 14 articles [sw22248]
  • Protein Data Bank (PDB) with a sequence identity cutoff <95%: 1996 distinct folds are found ... solved non-homologous proteins in PDB. For both folded and misfolded models, TM-align ... similarity of the model to the other proteins in the PDB. This correlation could...
  • NNcon

  • Referenced in 6 articles [sw17013]
  • contact map prediction is useful for protein folding rate prediction, model selection and 3D structure ... Eighth Critical Assessment of Techniques for Protein Structure Prediction (CASP8), 2008. Both NNcon server...
  • RAPTOR

  • Referenced in 19 articles [sw09002]
  • RApid Protein Threading by Operation Research technique. Large scale benchmark test for fold recognition shows ... fold similarity level. The CAFASP3 evaluation, a blind and public test by the protein structure ... recognition capability and alignment accuracy for Fold Recognition (FR) family targets. RAPTOR also performs very...
  • MAMMOTH

  • Referenced in 11 articles [sw26215]
  • describe random structural alignments of proteins with different folds with good accuracy by an extreme ... observation, a structural similarity score between two proteins or two different conformations of the same...
  • RSARF

  • Referenced in 5 articles [sw22442]
  • problem. The complete physicochemical understanding of protein folding is essential for the accurate structure prediction ... residue solvent accessibility gives useful insights into protein structure prediction and function prediction. In this...
  • FORESST

  • Referenced in 3 articles [sw26866]
  • recognizing the three-dimensional fold from the protein amino acid sequence based on a combination ... Beta and Alpha-Beta class proteins. Compared to other fold recognition methods based on HMMs ... acid sequence of a query protein. The predicted fold of a query protein ... capture important information about the fold of a protein embedded in the length and arrangement...
  • iMethyl-PseAAC

  • Referenced in 21 articles [sw22443]
  • Acid Composition Approach. Before becoming the native proteins during the biosynthesis, their polypeptide chains created ... cutting, folding, and posttranslational modification (PTM). Knowledge of PTMs in proteins is crucial for dynamic...
  • GenThreader

  • Referenced in 10 articles [sw35746]
  • Fold Recognition (GenTHREADER). GenThreader: Detect distant homology to proteins of known structure; Compare a sequence...
  • FoldIndex

  • Referenced in 5 articles [sw35528]
  • described: it predicts if a given protein sequence is intrinsically unfolded implementing the algorithm ... rate comparable to that of more sophisticated fold prediction methods. Sliding windows permit identification ... large regions within a protein that possess folding propensities different from those of the whole...
  • SCPRED

  • Referenced in 6 articles [sw26876]
  • some protein chains that share twilight-zone pairwise identity can form similar folds and thus ... structure prediction. The folding type of a protein or its domain is defined ... sequence. Tests performed with datasets of 1673 protein chains, in which any pair of sequences ... processing filter to improve performance of modern fold classification methods...
  • FoldX

  • Referenced in 9 articles [sw21771]
  • mutations on the stability, folding and dynamics of proteins and nucleic acids. The core functionality...
  • CONFOLD

  • Referenced in 1 article [sw17008]
  • Residue-residue contact-guided ab initio protein folding. Predicted protein residue–residue contacts ... dimensional models and consequently to predict protein folds from scratch. A considerable amount of effort ... whereas few methods are available to construct protein tertiary structures from predicted contacts ... Here, we present an ab initio protein folding method to build three-dimensional models using...
  • Apbsmem

  • Referenced in 4 articles [sw22298]
  • molecular interactions. They help guide the folding of proteins, increase the binding of one protein...
  • ConSeq

  • Referenced in 4 articles [sw35647]
  • important structural role in maintaining the protein’s fold. Thus, estimated evolutionary rates, as well...
  • MULTICOM

  • Referenced in 2 articles [sw15827]
  • prediction, protein beta-sheet structure prediction, protein fold recognition, multiple template combination, template-based structure...