• UniProt

  • Referenced in 136 articles [sw21320]
  • helpful in identifying which proteins are the best characterized and most informative for comparative analysis...
  • Cluster-C

  • Referenced in 6 articles [sw10932]
  • extraction of maximal cliques Although the characterization of proteins cannot solely rely upon sequence similarity...
  • PREvaIL

  • Referenced in 10 articles [sw25073]
  • critical to our understanding the relationship between protein sequence, structure, function, and enhancing our ability ... structures determined, experimental methods for enzyme functional characterization lag behind. Because experimental methods used ... sequence-structure-function relationships of proteins and facilitating the characterization of novel enzymes lacking functional...
  • Profunc

  • Referenced in 3 articles [sw17204]
  • motifs or close relationships to functionally characterized proteins. A summary of the analyses provides...
  • FASTA3

  • Referenced in 7 articles [sw15724]
  • become routine steps in biochemical characterization, from newly cloned proteins to entire genomes...
  • ProtorP

  • Referenced in 2 articles [sw35300]
  • server provides an efficient way of characterizing proteinprotein associations of new or existing proteins...
  • ProteoWizard

  • Referenced in 2 articles [sw30165]
  • been developed to identify and quantify the proteins in biological and clinical samples1, identify pathways ... endogenous and exogenous perturbations2, and characterize protein complexes3. Despite successes, the interpretation of vast proteomics...
  • Helanal

  • Referenced in 5 articles [sw29681]
  • Helanal: A program to characterize helixgeometry in proteins. A detailed analysis of structural and position...
  • SCOWLP

  • Referenced in 3 articles [sw35413]
  • based database for detailed characterization and visualization of protein interfaces. SCOWLP (S tructural C haracterization ... relational database for detailed characterization and visualization of the PDB protein interfaces. The SCOWLP database...
  • CyclinPred

  • Referenced in 1 article [sw22405]
  • sequences with low similarity to well characterized protein sequences is a major challenge of computational ... family is once such important family of proteins which consists of sequences with low sequence ... represent all of the identified and characterized cyclin sequences. We describe a Support Vector Machine ... features of selected cyclin and non cyclin protein sequences. The training features of the protein...
  • ConSurf

  • Referenced in 5 articles [sw35754]
  • grades onto the molecular surface of these proteins reveals patches of highly conserved (or occasionally ... used for high-throughput characterization of functional regions in proteins. Availability: The ConSurf web server...
  • SCOP2

  • Referenced in 1 article [sw16875]
  • successor to the Structural Classification of Proteins (SCOP, http://scop.mrc-lmb.cam.ac.uk/scop/) database. Similarly to SCOP ... SCOP2 is to organize structurally characterized proteins according to their structural and evolutionary relationships. SCOP2...
  • PathBLAST

  • Referenced in 9 articles [sw29737]
  • protein interaction pathways based on similarity to the network of another, well-characterized species. PathBLAST ... this implementation, the user specifies a short protein interaction path for query against a target...
  • HIPPIE

  • Referenced in 5 articles [sw29288]
  • information on particular proteins. In many analyses the reliability of the characterization of the interactions ... this goal, we generated HIPPIE (Human Integrated Protein-Protein Interaction rEference), a human PPI dataset ... correlate to the quality of the experimental characterization. The HIPPIE web tool (available ... true PPI sets by generating subnetworks around proteins of interest at a specified confidence level...
  • KNOTTIN

  • Referenced in 2 articles [sw26871]
  • imaging. These widespread and functionally diverse proteins are characterized by the presence of three interwoven...
  • TRAJELIX

  • Referenced in 1 article [sw10942]
  • Computational Tool for the Geometric Characterization of Protein Helices During Molecular Dynamics Simulations. We have ... geometric characterization of distorted conformations of alpha-helices proteins, such as those that can potentially...
  • PredGPI

  • Referenced in 3 articles [sw17176]
  • site. Computational methods were developed to discriminate proteins that undergo this post-translational modification starting ... redundant dataset of experimentally characterized GPI-anchored proteins whose annotation was carefully checked...
  • PONDR-FIT

  • Referenced in 2 articles [sw16904]
  • meta-predictor of intrinsically disordered amino acids. Protein intrinsic disorder is becoming increasingly recognized ... many different experimental methods for characterizing intrinsically disordered proteins and regions; nevertheless, the prediction...
  • ProDy

  • Referenced in 4 articles [sw24072]
  • structure-based analysis of protein dynamics. ProDy allows for quantitative characterization of structural variations ... given family or subfamily of proteins, their mutants and sequence homologues, in the presence/absence...
  • NNScore

  • Referenced in 2 articles [sw19736]
  • Network-Based Scoring Function for the Characterization of Protein-Ligand Complexes. As high-throughput biochemical ... human mind at receptor-ligand complex characterization, we here present two scoring functions based...