• TETRAD

  • Referenced in 369 articles [sw12177]
  • which creates, simulates data from, estimates, tests, predicts with, and searches for causal and statistical ... structure, and to search for linear feedback models--and in the ability to calculate predictions ... certainly to correct information about the true structure in the large sample limit, provided that...
  • GAUSSIAN

  • Referenced in 170 articles [sw06118]
  • Gaussian is an electronic structure program, used by chemists, chemical engineers, biochemists, physicists and others ... laws of quantum mechanics, Gaussian predicts the energies, molecular structures, and vibrational frequencies of molecular...
  • GOLEM

  • Referenced in 51 articles [sw24695]
  • real-world problems such as protein structure prediction and finite element mesh design. GOLEM copes...
  • ViennaRNA

  • Referenced in 20 articles [sw10504]
  • secondary structures. RNA secondary structure prediction through energy minimization is the most used function ... 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...
  • propy

  • Referenced in 27 articles [sw22402]
  • been frequently used for analysing and predicting structural, functional, expression and interaction profiles of proteins...
  • RAPTOR

  • Referenced in 19 articles [sw09002]
  • protein 3-dimensional (3D) structure prediction via threading. Based on the contact map graph ... public test by the protein structure prediction community, ranks RAPTOR as top 1, among individual...
  • PSIPRED

  • Referenced in 14 articles [sw11340]
  • PSIPRED protein structure prediction server. The PSIPRED protein structure prediction server allows users to submit ... sequence: PSIPRED, a highly accurate secondary structure prediction method; MEMSAT 2, a new version...
  • Pfold

  • Referenced in 12 articles [sw23813]
  • Hein, J. J.: Pfold: RNA secondary structure prediction using stochastic context-free grammars. RNA secondary ... many biological processes and efficient structure prediction can give vital directions for experimental investigations. Many ... available programs for RNA secondary structure prediction only use a single sequence at a time ... model and a probabilistic model of structures. Predictions can be done on a web server...
  • TM-align

  • Referenced in 14 articles [sw22248]
  • applied to an all-against-all structure comparison of 10 515 representative protein chains from ... align to match the models predicted by TASSER for solved non-homologous proteins ... correlation between the correctness of the predicted structure and the structural similarity of the model ... model selection in blind protein structure predictions. The TM-align program is freely downloadable...
  • I-TASSER

  • Referenced in 13 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...
  • bmrm

  • Referenced in 18 articles [sw11016]
  • data analysis. The applications includes: structured prediction, linear SVM, multi-class SVM, f-beta optimization...
  • System Identification Toolbox

  • Referenced in 160 articles [sw05686]
  • parametric, subspace-based, and prediction-error algorithms coupled (in the latter case) with either MIMO ... state space or MISO polynomial model structures. A key feature of the software...
  • Mfold

  • Referenced in 39 articles [sw12672]
  • Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids...
  • SVMstruct

  • Referenced in 28 articles [sw04075]
  • Vector Machine (SVM) algorithm for predicting multivariate or structured outputs. It performs supervised learning...
  • CONTRAfold

  • Referenced in 8 articles [sw17117]
  • strategy for single sequence RNA secondary structure prediction. More recently, stochastic context-free grammars (SCFGs ... alternative probabilistic methodology for modeling RNA structure. Unlike physics-based methods, which rely on thousands ... models. CONTRAfold is a novel secondary structure prediction method based on conditional log-linear models ... thermodynamic parameters for RNA secondary structure prediction...
  • Quat-2L

  • Referenced in 15 articles [sw22469]
  • server for predicting protein quaternary structural attributes. By hybridizing the functional-domain and sequence-correlated ... Quat-2L” was developed for predicting the quaternary structural attribute of a protein according ... homo-oligomer or hetero-oligomer, then the prediction will be automatically continued to further identify...
  • SCPRED

  • Referenced in 6 articles [sw26876]
  • similarity with predicting sequences. Background: Protein structure prediction methods provide accurate results when a homologous ... similarity would be desirable for the structure prediction. The folding type of a protein ... defined as the structural class. Current structural class prediction methods that predict the four structural ... information extracted from the secondary structure predicted with PSI-PRED and one feature computed from...
  • 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...
  • MAMMOTH

  • Referenced in 10 articles [sw26215]
  • Advances in structural genomics and protein structure prediction require the design of automatic, fast, objective ... similarity of low-resolution three-dimensional structures, via experimental or theoretical approaches. Here...
  • 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...