• PSI-BLAST

  • Referenced in 231 articles [sw17324]
  • BLAST: a new generation of protein database search programs. The BLAST programs are widely used ... tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety...
  • KEGG

  • Referenced in 265 articles [sw13866]
  • molecular building blocks of genes and proteins (genomic information) and chemical substances (chemical information) that...
  • BLAST

  • Referenced in 247 articles [sw17334]
  • biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates...
  • UniProt

  • Referenced in 131 articles [sw21320]
  • UniProt: a hub for protein information. UniProt is an important collection of protein sequences ... relative amount of knowledge known about each protein. These scores will be helpful in identifying ... which proteins are the best characterized and most informative for comparative analysis. All UniProt data...
  • Cell-PLoc

  • Referenced in 90 articles [sw09126]
  • servers for predicting subcellular localization of proteins in various organisms. Information on subcellular localization ... proteins is important to molecular cell biology, proteomics, system biology and drug discovery. To provide ... positive bacterial, Gram-negative bacterial and viral proteins, respectively. Using these Web servers ... sites and in which none of the proteins included had greater than or equal to25...
  • APBS

  • Referenced in 88 articles [sw05766]
  • simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics, implicit solvent ... binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants...
  • Cytoscape

  • Referenced in 76 articles [sw09080]
  • used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that ... changes in gene expression, a study of protein complexes involved in cellular recovery...
  • Gromacs

  • Referenced in 121 articles [sw04128]
  • primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have...
  • VMD

  • Referenced in 84 articles [sw18651]
  • analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies ... general molecules, as VMD can read standard Protein Data Bank (PDB) files and display...
  • Pfam

  • Referenced in 104 articles [sw23108]
  • services. Pfam is a database of protein families that currently contains 7973 entries (release...
  • MCODE

  • Referenced in 48 articles [sw35748]
  • method for finding molecular complexes in large protein interaction networks. Results: This paper describes ... that detects densely connected regions in large protein-protein interaction networks that may represent molecular ... outward traversal from a locally dense seed protein to isolate the dense regions according ... cluster interconnectivity, which is relevant for protein networks. Protein interaction and complex information from...
  • MIBPB

  • Referenced in 51 articles [sw08106]
  • between the biomolecule and the solvent. For protein molecular surfaces, which may possess troublesome geometrical ... MIBPB package are tested by protein–solvent solvation energy calculations and analysis of salt effects ... proteinprotein binding energies, respectively. © 2010 Wiley Periodicals, Inc. J Comput Chem...
  • Cd-hit

  • Referenced in 48 articles [sw16887]
  • clustering and comparing large sets of protein or nucleotide sequences. Motivation ... Bioinformatics, 18, 77–82) describing an ultrafast protein sequence clustering program called cd-hit. This ... program can efficiently cluster a huge protein database with millions of sequences. However, the applications ... underlying algorithm are not limited to only protein sequences clustering, here we present several...
  • Euk-mPLoc

  • Referenced in 42 articles [sw26860]
  • fusion classifier for large-scale eukaryotic protein subcellular location prediction by incorporating multiple sites ... critical challenges in predicting protein subcellular localization is how to deal with the case ... except for the one focused on the proteins in budding yeast only. For most existing ... predictors, the multiple-site proteins are either excluded from consideration or assumed even not existing...
  • Memtype-2L

  • Referenced in 39 articles [sw16472]
  • server for predicting membrane proteins and their types by incorporating evolution information through pse-PSSM ... Given an uncharacterized protein sequence, how can we identify whether it is a membrane protein ... which membrane protein type it belongs to? These questions are important because they are closely ... biological function of the query protein and to its interaction process with other molecules...
  • iSNO-PseAAC

  • Referenced in 39 articles [sw22446]
  • PseAAC: predict cysteine S-nitrosylation sites in proteins by incorporating position specific amino acid propensity ... amino acid composition. Posttranslational modifications (PTMs) of proteins are responsible for sensing and transducing signals ... universal PTMs. With the avalanche of protein sequences generated in the post-genomic ... timely identifying the exact SNO sites in proteins because this kind of information is very...
  • iLoc-Euk

  • Referenced in 37 articles [sw22434]
  • subcellular localization of singleplex and multiplex eukaryotic proteins. Predicting protein subcellular localization is an important ... difficult problem, particularly when query proteins may have the multiplex character, i.e., simultaneously exist ... subcellular location sites. Most of the existing protein subcellular location predictor can only be used ... deal with the single-location or ”singleplex” proteins. Actually, multiple-location or ”multiplex” proteins should...
  • TRANSFAC

  • Referenced in 74 articles [sw17201]
  • scaffold/matrix attached regions (S/MARs) and the proteins binding to them. Additionally, the databases TRANSPATH, about...
  • MUSCLE

  • Referenced in 73 articles [sw13193]
  • computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast...
  • iLoc-Hum

  • Referenced in 36 articles [sw22433]
  • scale to predict subcellular locations of human proteins with both single and multiple sites. Although ... made for predicting the subcellular locations of proteins based on their sequence information, it still ... challenging problem, particularly when query proteins may have the multiplex character, i.e., they simultaneously exist ... methods were established on the assumption: a protein has one, and only one, subcellular location...