• GOLEM

  • Referenced in 53 articles [sw24695]
  • real-world problems such as protein structure prediction and finite element mesh design. GOLEM copes...
  • RAPTOR

  • Referenced in 20 articles [sw09002]
  • programming approach to do protein 3-dimensional (3D) structure prediction via threading. Based ... blind and public test by the protein structure prediction community, ranks RAPTOR...
  • PSIPRED

  • Referenced in 15 articles [sw11340]
  • PSIPRED protein structure prediction server. The PSIPRED protein structure prediction server allows users to submit ... protein sequence, perform a prediction of their choice and receive the results of the prediction ... three prediction methods to apply to their sequence: PSIPRED, a highly accurate secondary structure prediction...
  • I-TASSER

  • Referenced in 18 articles [sw17207]
  • unified platform for automated protein structure and function prediction. The iterative threading assembly refinement ... integrated platform for automated protein structure and function prediction based on the sequence-to-structure ... contains full-length secondary and tertiary structure predictions, and functional annotations on ligand-binding sites ... state-of-the-art protein structure and function predictions. The server is available...
  • TM-align

  • Referenced in 15 articles [sw22248]
  • against-all structure comparison of 10 515 representative protein chains from the Protein Data Bank ... match the models predicted by TASSER for solved non-homologous proteins in PDB. For both ... predicted structure and the structural similarity of the model to the other proteins ... assist in model selection in blind protein structure predictions. The TM-align program is freely...
  • PseAAC-General

  • Referenced in 16 articles [sw22430]
  • used to represent protein sequences in predicting protein structural and functional attributes. We developed...
  • Quat-2L

  • Referenced in 15 articles [sw22469]
  • server for predicting protein quaternary structural attributes. By hybridizing the functional-domain and sequence-correlated ... developed for predicting the quaternary structural attribute of a protein according to its sequence information ... layer is to identify the query protein as monomer, homo-oligomer, or hetero-oligomer ... homo-oligomer or hetero-oligomer, then the prediction will be automatically continued to further identify...
  • MAMMOTH

  • Referenced in 11 articles [sw26215]
  • comparison. Advances in structural genomics and protein structure prediction require the design of automatic, fast ... structures, via experimental or theoretical approaches. Here, a new method for sequence-independent structural alignment ... presented that allows comparison of an experimental protein structure with an arbitrary low-resolution protein...
  • QMEAN

  • Referenced in 7 articles [sw17377]
  • estimation is an essential component of protein structure prediction, since ultimately the accuracy ... applications. Usually, in the course of protein structure prediction a set of alternative models...
  • SCPRED

  • Referenced in 6 articles [sw26876]
  • SCPRED: Accurate prediction of protein structural class for sequences of twilight ... zone similarity with predicting sequences. Background: Protein structure prediction methods provide accurate results when ... determining structural similarity without the sequence similarity would be desirable for the structure prediction ... protein or its domain is defined as the structural class. Current structural class prediction methods...
  • MaxSub

  • Referenced in 8 articles [sw35908]
  • automated measure for the assessment of protein structure prediction quality. Results: MaxSub...
  • GlobPlot

  • Referenced in 7 articles [sw06213]
  • structural genomics era is to predict protein structure and function, including identification of those proteins...
  • PSICOV

  • Referenced in 7 articles [sw17010]
  • PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments ... both structure and function prediction to name but two benefits. Sequence-based contact predictions ... predictions for a protein of length L) precision for long-range contacts (sequence separation ... significant benefit in protein structure prediction or model quality assessment. Availability: The PSICOV source code...
  • RSARF

  • Referenced in 5 articles [sw22442]
  • sequence using random forest method. Prediction of protein structure from its amino acid sequence ... physicochemical understanding of protein 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 ... useful for prediction of residue solvent accessibility from protein sequence without using structural information...
  • NNcon

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

  • Referenced in 7 articles [sw35977]
  • structure prediction server. An interactive protein secondary structure prediction Internet server is presented. The server...
  • 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 ... experiment (Critical Assessment of Techniques for Proteins Structural Prediction). Our alignment strategy obtains better results...
  • PROFEAT

  • Referenced in 14 articles [sw16924]
  • features of proteins and peptides from amino acid sequence. Sequence-derived structural and physicochemical features ... statistical learning models for predicting proteins and peptides of different structural, functional and interaction profiles ... composition, transition and distribution of various structural and physicochemical properties. In addition, it can also ... computed protein features have been used in a number of published works for predicting proteins...
  • propy

  • Referenced in 27 articles [sw22402]
  • analysing and predicting structural, functional, expression and interaction profiles of proteins and peptides. To facilitate...
  • HOPE

  • Referenced in 4 articles [sw32999]
  • HOPE: A homotopy optimization method for protein structure prediction. We use a homotopy optimization method ... minimize the potential energy associated with a protein model. The method uses the minimum energy ... protein as a template to predict the lowest energy structure of a query sequence. This ... predicting correct structures. Successful results are presented for pairs of homologous proteins, where HOPE...