• MODELLER

  • Referenced in 33 articles [sw27731]
  • MODELLER: A Program for Protein Structure Modeling. MODELLER is used for homology or comparative modeling ... hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints ... protein structures, optimization of various models of protein structure with respect to a flexibly defined ... sequence databases, comparison of protein structures, etc. MODELLER is available for download for most Unix/Linux...
  • SWISS-MODEL

  • Referenced in 14 articles [sw17373]
  • SWISS-MODEL: An automated protein homology-modeling server. SWISS-MODEL (http://swissmodel.expasy.org) is a server ... automated comparative modeling of three-dimensional (3D) protein structures. It pioneered the field of automated ... user requests for 3D protein models. SWISS-MODEL provides several levels of user interaction through ... sequence of a protein is submitted to build a 3D model. Template selection, alignment...
  • Cytoscape

  • Referenced in 69 articles [sw09080]
  • Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks. Cytoscape is an open ... used in conjunction with large databases of protein ... protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms ... changes in gene expression, a study of protein complexes involved in cellular recovery...
  • Pse-in-One

  • Referenced in 41 articles [sw22407]
  • such as DNA, RNA or protein) with a discrete model or a vector that ... possible feature vectors for DNA, RNA and protein sequences. Particularly, it can also generate those...
  • VMD

  • Referenced in 83 articles [sw18651]
  • designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid...
  • MAMMOTH

  • Referenced in 11 articles [sw26215]
  • automated method for model comparison. Advances in structural genomics and protein structure prediction require ... structure with an arbitrary low-resolution protein tertiary model. The heuristic algorithm is given ... describe random structural alignments of proteins with different folds with good accuracy by an extreme ... routine use with large databases of protein models. Overall, our results indicate that...
  • TM-align

  • Referenced in 14 articles [sw22248]
  • representative protein chains from the Protein Data Bank (PDB) with a sequence identity cutoff ... match the models predicted by TASSER for solved non-homologous proteins in PDB. For both ... structural similarity of the model to the other proteins in the PDB. This correlation could ... used to assist in model selection in blind protein structure predictions. The TM-align program...
  • iDNA-Prot

  • Referenced in 16 articles [sw22410]
  • using random forest with grey model. DNA-binding proteins play crucial roles in various cellular ... that were extracted from protein sequences via the ”grey model” and by adopting the random ... predictor, called iDNA-Prot, for identifying uncharacterized proteins as DNA-binding proteins...
  • PROTEIN

  • Referenced in 15 articles [sw21342]
  • PROTEIN, a PROver with a Theory INterface. PROTEIN (PROver with a Theory Extension INterface ... Besides various standard-refinements known for model elimination, PROTEIN also offers a variant of model...
  • I-TASSER

  • Referenced in 18 articles [sw17207]
  • server is an integrated platform for automated protein structure and function prediction based ... models from multiple threading alignments and iterative structural assembly simulations. The function of the protein ... structurally matching the 3D models with other known proteins. The output from a typical server ... based on the confidence score of the modeling. This protocol provides new insights and guidelines...
  • PseAAC

  • Referenced in 30 articles [sw16469]
  • composition can represent a protein sequence in a discrete model without completely losing its sequence ... improving the prediction quality for various protein attributes. However, dealing with different problems may need...
  • QMEAN

  • Referenced in 7 articles [sw17377]
  • QMEAN server for protein model quality estimation. Model quality estimation is an essential component ... protein structure prediction, since ultimately the accuracy of a model determines its usefulness for specific ... course of protein structure prediction a set of alternative models is produced, from which subsequently...
  • STRING

  • Referenced in 26 articles [sw23938]
  • direct and indirect interactions between proteins in a given cell would represent an important milestone ... made—particularly for certain model organisms and functional systems. Currently, protein interactions and associations ... scored and integrated, resulting in comprehensive protein networks covering >1100 organisms. Here, we describe ... algorithm for transferring interactions from one model organism to the other; and (iii) we provide...
  • PROFEAT

  • Referenced in 14 articles [sw16924]
  • computing structural and physicochemical features of proteins and peptides from amino acid sequence. Sequence-derived ... development of statistical learning models for predicting proteins and peptides of different structural, functional...
  • DPP-PseAAC

  • Referenced in 5 articles [sw24764]
  • PseAAC: a DNA-binding protein prediction model using Chou’s general pseaac. A DNA-binding ... methods are sought for predicting whether a protein can bind with ... accurate way. Our model extracts meaningful information directly from the protein sequences, without any dependence ... method, named as {it DNA-binding Protein Prediction model using Chou’s general PseAAC...
  • APBS

  • Referenced in 87 articles [sw05766]
  • most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media ... simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics, implicit solvent...
  • HOPE

  • Referenced in 4 articles [sw32999]
  • potential energy associated with a protein model. The method uses the minimum energy conformation...
  • SDA

  • Referenced in 4 articles [sw08089]
  • diffusion-controlled. Simulations of model proteins show that diffusion-limited association rates are approximately...
  • GeneMarkS

  • Referenced in 6 articles [sw23024]
  • prediction can be improved by combining models of protein-coding and non-coding regions ... gene start within an iterative Hidden Markov model based algorithm. The new gene prediction method ... genome with no prior knowledge of any protein or rRNA genes. The GeneMarkS implementation uses ... gene finding program GeneMark.hmm, heuristic Markov models of coding and non-coding regions...
  • OOgenesis_Pred

  • Referenced in 5 articles [sw25083]
  • great interest. However, the experimental determination of proteins involved in oogenesis is expensive, time consuming ... powerful discriminating model is indispensable for classifying oogenesis/non-oogenesis-related proteins with high accuracy and precision. Hereby ... oogenesis proteins. By means of informative protein physicochemical properties and in addition parameter optimization scheme ... encouraging and strong model for predicting proteins involved in oogenesis with appropriate performance. To enhance...