• 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...
  • 2D-MH

  • Referenced in 21 articles [sw19727]
  • called “2D-MH”, is proposed to represent protein sequences. It is formed by incorporating ... better reflecting the innate structure of the protein sequence, (3) clear visibility in displaying...
  • MemHyb

  • Referenced in 15 articles [sw25194]
  • against membrane proteins. Knowledge of membrane protein’s structure and function has great importance ... help in identifying the new membrane protein types based on their primary sequence. In this...
  • 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 a homologous protein is predicted ... absence of homologous templates. However, some protein chains that share twilight-zone pairwise identity ... desirable for the structure prediction. The folding type of a protein or its domain...
  • MDAnalysis

  • Referenced in 9 articles [sw17696]
  • dynamics (MD) simulation trajectories and individual protein structures. It is written in the Python language ... CHARMM, Gromacs, Amber, and NAMD and the Protein Data Bank format can be read...
  • FUGUE

  • Referenced in 9 articles [sw16894]
  • program for recognizing distant homologues by sequence-structure comparison (http://www-cryst.bioc.cam.ac.uk/fugue/), has three ... amino acid in a protein structure are constrained by its local structural environment, which...
  • GlobPlot

  • Referenced in 7 articles [sw06213]
  • structural genomics era is to predict protein structure and function, including identification of those proteins ... corresponding to globular proteins, as needed for many biochemical studies, particularly structural biology. GlobPlot...
  • PREvaIL

  • Referenced in 10 articles [sw25073]
  • approach for inferring catalytic residues using sequence, structural, and network features in a machine-learning ... understanding the relationship between protein sequence, structure, function, and enhancing our ability to design novel ... both understanding the complex sequence-structure-function relationships of proteins and facilitating the characterization...
  • PDB-REPRDB

  • Referenced in 5 articles [sw26865]
  • number of entries including membrane protein structures in the PDB has increased rapidly with determination ... numbers of membrane protein structures because of improved X-ray crystallography, NMR, and electron microscopic ... experimental techniques. Since many protein structure studies must address globular and membrane proteins separately, this...
  • VADAR

  • Referenced in 6 articles [sw12496]
  • analyzing and assessing peptide and protein structures from their PDB coordinate data. The results have ... graphs for quantitatively and qualitatively assessing protein structures determined by X-ray crystallography, NMR spectroscopy...
  • PFRES

  • Referenced in 6 articles [sw26875]
  • information and predicted secondary structure. MOTIVATION: The number of protein families has been estimated ... slowing down. This indicates that the protein structure space will be soon covered and thus ... proteins that share twilight-zone sequence identity can form similar folds. Therefore, determination of structural ... prediction of tertiary structures. RESULTS: The proposed PFRES method for automated protein fold classification from...
  • RSARF

  • Referenced in 5 articles [sw22442]
  • using random forest method. Prediction of protein structure from its amino acid sequence is still ... 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 ... residue solvent accessibility from protein sequence without using structural information. The RSARF program, datasets...
  • OXBench

  • Referenced in 7 articles [sw22988]
  • guide in the prediction of the protein structure and in identifying key functional residues, however ... derived from the comparison of protein three-dimensional structures together with evaluation measures and software...
  • GenBank

  • Referenced in 8 articles [sw28961]
  • databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal...
  • MaxSub

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

  • Referenced in 7 articles [sw17010]
  • PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments ... protein, remains an open problem in the field of structural bioinformatics. Interest in this long ... Progress could have major impacts in both structure and function prediction to name ... significant benefit in protein structure prediction or model quality assessment. Availability: The PSICOV source code...
  • iPhos-PseEvo

  • Referenced in 17 articles [sw23953]
  • human body by altering the structural conformation of a protein, causing it to become activated/deactivated...
  • ESyPred3D

  • Referenced in 5 articles [sw16876]
  • ESyPred3D: Prediction of proteins 3D structures. Motivation: Homology or comparative modeling is currently the most ... method to predict the three-dimensional structure of proteins. It generally consists in four steps ... multiple alignment programs. The final three-dimensional structure is build using the modeling package MODELLER ... experiment (Critical Assessment of Techniques for Proteins Structural Prediction). Our alignment strategy obtains better results...
  • SSAP

  • Referenced in 7 articles [sw08918]
  • Method for automatically comparing three dimensional protein structures using double dynamic programming...
  • ProTherm

  • Referenced in 9 articles [sw16247]
  • Release 4.0 of ProTherm, thermodynamic database for proteins and mutants, contains ∼14 500 numerical data ... along with experimental methods and conditions, and structural, functional ... literature information. The sequence and structural information of proteins is connected with thermodynamic data through ... replacements and links to homologous structures to each protein. Further, we have improved the search...