• MIBPB

  • Referenced in 49 articles [sw08106]
  • software package, the MIBPB solver, for electrostatic analysis. The MIBPB has a unique feature that ... between the biomolecule and the solvent. For protein molecular surfaces, which may possess troublesome geometrical ... solvation energy calculations and analysis of salt effects on proteinprotein binding energies, respectively...
  • UniProt

  • Referenced in 128 articles [sw21320]
  • identifying which proteins are the best characterized and most informative for comparative analysis. All UniProt...
  • LSTM

  • Referenced in 24 articles [sw03373]
  • keyword spotting, music composition, attentive vision, protein analysis, stock market prediction, and many other sequence...
  • MEGA

  • Referenced in 32 articles [sw09078]
  • biologist-centric software for evolutionary analysis of DNA and protein sequences. The Molecular Evolutionary Genetics ... desktop application designed for comparative analysis of homologous gene sequences either from multigene families ... protein evolution. In addition to the tools for statistical analysis of data, MEGA provides many...
  • VMD

  • Referenced in 83 articles [sw18651]
  • modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies...
  • IntAct

  • Referenced in 29 articles [sw21665]
  • toolkit for the storage, presentation and analysis of protein interactions. The web interface provides both...
  • ExPASy

  • Referenced in 14 articles [sw34228]
  • analysis. The ExPASy (the Expert Protein Analysis System) World Wide Web server (http://www.expasy.org ... databases and analytical tools dedicated to proteins and proteomics. ExPASy databases include SWISS-PROT ... PROSITE, ENZYME and the SWISS-MODEL repository. Analysis tools are available for specific tasks relevant...
  • GPCR-GIA

  • Referenced in 19 articles [sw22458]
  • their families with grey incidence analysis. G-protein-coupled receptors (GPCRs) play fundamental roles...
  • 2D-MH

  • Referenced in 21 articles [sw19727]
  • server for generating graphic representation of protein sequences based on the physicochemical properties of their ... analysis. Here, a new two-dimensional graph, called “2D-MH”, is proposed to represent protein ... metric for the “evolutionary distance” of a protein from one species to the other ... vehicle for large-scale analysis of the avalanche of protein sequences generated in the post...
  • Psortb

  • Referenced in 18 articles [sw11344]
  • bacterial protein subcellular localization and insights gained from comparative proteome analysis. Motivation: PSORTb v.1.1 ... comparative analysis of localization. Results: An expanded database of proteins of known localization ... whole proteome analysis. We show that the proportion of proteins at each localization is remarkably...
  • Gpos-PLoc

  • Referenced in 11 articles [sw26870]
  • localization of Gram-positive bacterial proteins. A statistical analysis indicated that ... eliminate redundancy and homology bias, only those proteins which have < 25% sequence identity ... vehicle for expediting the analysis of Gram-positive bacterial proteins. Gpos-PLoc is freely accessible...
  • MC73

  • Referenced in 7 articles [sw12394]
  • that include matrix reordering, graph partitioning, protein analysis, data mining, machine learning, and web search...
  • BioGRID

  • Referenced in 46 articles [sw17422]
  • protein and genetic interactions is critical for interrogation of gene/protein function and analysis of global ... file formats. User-customized graphs with embedded protein, gene and interaction attributes can be constructed...
  • iMethyl-PseAAC

  • Referenced in 21 articles [sw22443]
  • Knowledge of PTMs in proteins is crucial for dynamic proteome analysis of various human diseases ... arginine or lysine, respectively. Given a protein, which site...
  • PIPE

  • Referenced in 6 articles [sw26869]
  • predict novel protein-protein interactions. We then used PIPE analysis to investigate the internal architecture ... gene deletion strains combined with TAP tagging analysis indicated that the deletion of a member ... PIPE can be used to analyse yeast proteins for which TAP tagging fails, thereby allowing ... tagging projects. Conclusion: PIPE analysis can predict yeast protein-protein interactions. Also, PIPE analysis...
  • FASTA

  • Referenced in 25 articles [sw09655]
  • FASTP and FASTA were designed to identify protein sequences that have descended from a common ... analysis and the biological context are required. In the course of analyzing the G-protein ... coupled receptor family, several proteins were found that, because with optimization, appeared to be members ... family which were not previously recognized. RDF2 analysis showed borderline z values, and only...
  • iDNA-Prot

  • Referenced in 16 articles [sw22410]
  • benchmark dataset in which none of the proteins included has ≥25% pairwise sequence identity ... throughput tool for large-scale analysis of DNA-binding proteins. As a user-friendly...
  • bioNMF

  • Referenced in 6 articles [sw14438]
  • that implements the NMF methodology in different analysis contexts to support some of the most ... clustering and biclustering gene expression data, protein sequence analysis, text mining of biomedical literature...
  • PAML

  • Referenced in 40 articles [sw10916]
  • Phylogenetic Analysis by Maximum Likelihood (PAML). PAML is a package of programs for phylogenetic analyses ... protein sequences using maximum likelihood. It is maintained and distributed for academic use free...
  • CellProfiler

  • Referenced in 14 articles [sw18751]
  • designed for flexible, high-throughput cell image analysis, CellProfiler. CellProfiler can address a variety ... example, cell count, size, per-cell protein levels) and complex morphological assays (for example, cell/organelle...