• VMD

  • Referenced in 90 articles [sw18651]
  • biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used ... general molecules, as VMD can read standard Protein Data Bank (PDB) files and display...
  • I-TASSER

  • Referenced in 18 articles [sw17207]
  • platform for automated protein structure and function prediction. The iterative threading assembly refinement (I-TASSER ... server is an integrated platform for automated protein structure and function prediction based ... alignments and iterative structural assembly simulations. The function of the protein is then inferred...
  • UniProt

  • Referenced in 136 articles [sw21320]
  • information. UniProt is an important collection of protein sequences and their annotations, which has doubled ... proteome identifier that uniquely identifies a particular assembly of a species and strain or subspecies ... relative amount of knowledge known about each protein. These scores will be helpful in identifying...
  • MEGA

  • Referenced in 35 articles [sw09078]
  • evolutionary relationships and patterns of DNA and protein evolution. In addition to the tools ... MEGA provides many convenient facilities for the assembly of sequence data sets from files...
  • PAnnBuilder

  • Referenced in 2 articles [sw32710]
  • package to automatically assemble protein annotation information from public resources to provide uniform annotation data...
  • Pathway Commons

  • Referenced in 9 articles [sw23072]
  • reactions, complex assembly, transport and catalysis events and physical interactions involving proteins, DNA, RNA, small...
  • BLAT

  • Referenced in 36 articles [sw16891]
  • mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when ... only be computed once for each genome assembly. BLAT has several major stages. It uses...
  • ZDOCK

  • Referenced in 6 articles [sw12737]
  • body search of docking orientations between two proteins. The current version, 3.0.2, includes performance optimization ... modification of ZDOCK to predict symmetric assemblies using the structure of a subunit...
  • 3DCoffee

  • Referenced in 7 articles [sw12008]
  • protein sequences and structures within multiple sequence alignments. Most bioinformatics analyses require the assembly ... developed 3DCoffee, a novel method for combining protein sequences and structures in order to generate...
  • ScalaBLAST

  • Referenced in 7 articles [sw08812]
  • unlocking protein information embedded in the genetic code, making it possible to assemble a ”tree...
  • MOCAT

  • Referenced in 1 article [sw23026]
  • programs to quality control, map, and assemble reads from metagenomic samples sequenced at a depth ... billion base pairs, and predict protein-coding genes on assembled metagenomes. Mapping against reference databases...
  • MATRAS

  • Referenced in 4 articles [sw16871]
  • multiple 3D alignment, which compares several protein structures. This program employs the progressive alignment algorithm ... which pairwise 3D alignments are assembled in the proper order. The third service ... server provides useful tools for insights into protein 3D structures...
  • Zyggregator

  • Referenced in 1 article [sw31179]
  • major problem in the preparation of recombinant proteins in biotechnology. Major advances in understanding ... rates of growth of the misfolded assemblies and the specific regions of the sequences that ... shown that the toxicity in vivo of protein aggregates can be predicted by estimating ... propensity of polypeptide chains to form protofibrillar assemblies. In this tutorial review we describe...
  • ADP_EM

  • Referenced in 3 articles [sw16893]
  • fast growth of atomic models of protein domains from crystallography or comparative modeling ... resolution density maps of larger molecular assemblies. Here, we report a novel fitting algorithm...
  • UpGene

  • Referenced in 3 articles [sw17355]
  • algorithm combination, together with PCR-based gene assembly, we have successfully optimized gene sequences ... immunodeficiency virus (SIV) strain mac239 structural antigenic proteins gag and env, resulting in high-level...
  • TaxMan

  • Referenced in 1 article [sw35407]
  • allow rapid assembly, storage and analysis of large aligned DNA and protein sequence datasets...
  • PacthDock

  • Referenced in 6 articles [sw12399]
  • input is two molecules of any type: proteins, DNA, peptides, drugs. The output ... Computer Vision. Docking can be compared to assembling a jigsaw puzzle. When solving the puzzle...
  • IntelliGEN

  • Referenced in 5 articles [sw01545]
  • distributed workflow system for discovering protein-protein interactions A large genomics project involves a significant ... entirely automatically by the computer (e.g. sequence assembly). It has become apparent that managing such ... laboratory is the discovery of protein-protein interactions of fungi, specifically Neurosporacrassa. We present...
  • MARCH-INSIDE

  • Referenced in 4 articles [sw27730]
  • uses of mt-sto-TIs to assemble drug-drug similarity Complex Networks of antimicrobial compounds ... generate macromolecular TIs and TPGIs for proteins or RNA targets for antimicrobial drugs...
  • PolySearch

  • Referenced in 1 article [sw16755]
  • proteinprotein interaction identification and disease gene identification using a variety of manually assembled ‘gold...