• iPfam

  • Referenced in 8 articles [sw29349]
  • Pfam domain interactions based on known 3D structures that are found in the Protein Data ... molecular level. Previously, the iPfam domaindomain interaction data was integrated within the Pfam database...
  • IDDI

  • Referenced in 1 article [sw29369]
  • domain level enriches valuable information about binding mechanism and functional role of interacting proteins ... 3D structures of complex proteins are reliable source of domain-domain interaction...
  • Rate4Site

  • Referenced in 7 articles [sw35756]
  • homologous proteins onto the molecular surface of one of the homologues whose 3D-structure ... potency, we study the Src SH2 domain. Like previously established methods, Rate4Site detected ... inter-domain interactions between the SH2 domain and the rest of the Src protein that...
  • CMView

  • Referenced in 2 articles [sw35120]
  • CMView: Interactive contact map visualization and analysis. Summary: Contact maps are a valuable visualization tool ... display proteins in two dimensions and to quickly identify structural features such as domain architecture ... which integrates rich contact map analysis with 3D visualization using PyMol. Our tool provides functions ... basic editing, visualization in contact map and 3D space and structural comparison with different built...
  • PlantTFDB

  • Referenced in 4 articles [sw17023]
  • each identified TF, including functional domains, 3D structures, gene ontology (GO), plant ontology (PO), expression ... curated functional description, binding motifs, regulation information, interaction, references, and cross-linsk to various databases ... prediction server, which supports both protein and nucleic acid sequences, has been...
  • HPMV

  • Referenced in 1 article [sw17017]
  • FASTA sequences. As output, HPMV provides an interactive cartoon showing the mutations in relation ... sequence architecture. A large variety of protein sequence architectural features were selected for their particular ... multiple sequence alignments of conserved domains and a simple 3D viewer mapping the mutation ... targeting signal), this interpretation is suggested. The interactive cartoon can be downloaded as standalone viewer...
  • CGAL

  • Referenced in 355 articles [sw00118]
  • The goal of the CGAL Open Source Project...
  • LAPACK

  • Referenced in 1626 articles [sw00503]
  • LAPACK is written in Fortran 90 and provides...
  • Maple

  • Referenced in 5040 articles [sw00545]
  • The result of over 30 years of cutting...
  • Mathematica

  • Referenced in 5883 articles [sw00554]
  • Almost any workflow involves computing results, and that...
  • Matlab

  • Referenced in 12074 articles [sw00558]
  • MATLAB® is a high-level language and interactive...
  • R

  • Referenced in 8359 articles [sw00771]
  • R is a language and environment for statistical...
  • REDUCE

  • Referenced in 739 articles [sw00789]
  • REDUCE is an interactive system for general algebraic...
  • AUTO

  • Referenced in 877 articles [sw01059]
  • AUTO is a software for continuation and bifurcation...
  • SNOPT

  • Referenced in 507 articles [sw02300]
  • SNOPT: An SQP algorithm for large-scale constrained...
  • MIRA

  • Referenced in 1 article [sw02392]
  • MIRA is a multi-pass DNA sequence data...
  • STAR

  • Referenced in 12 articles [sw02515]
  • STAR: ultrafast universal RNA-seq aligner. Motivation: Accurate...
  • NEURON

  • Referenced in 178 articles [sw03059]
  • Parallel network simulations with NEURON. The NEURON simulation...
  • CUDA

  • Referenced in 1185 articles [sw03258]
  • The NVIDIA® CUDA® Toolkit provides a comprehensive development...
  • deal.ii

  • Referenced in 549 articles [sw03516]
  • deal.II is a C++ program library targeted at...