• SparseMatrix

  • Referenced in 608 articles [sw04629]
  • problems with underlying 2D or 3D geometry (as structural engineering, computational fluid dynamics, model reduction...
  • FreeFem++

  • Referenced in 1010 articles [sw01436]
  • 3d) from several branches of physics such as fluid-structure interactions require interpolations of data...
  • CGAL

  • Referenced in 350 articles [sw00118]
  • structures and algorithms like triangulations (2D constrained triangulations and Delaunay triangulations in 2D and 3D ... convex hull algorithms (in 2D, 3D and dD), search structures (kd trees for nearest neighbor...
  • SBA

  • Referenced in 24 articles [sw05242]
  • reconstruction vision algorithm to obtain optimal 3D structure and motion (i.e. camera matrix) parameter estimates ... initial estimates, BA simultaneously refines motion and structure by minimizing the reprojection error between ... 3D points and cameras results in the underlying normal equations exhibiting a sparse block structure ... parameters describing cameras and 3D structure. Therefore, it can support virtually any manifestation/parameterization...
  • AutoDock

  • Referenced in 34 articles [sw09659]
  • bind to a receptor of known 3D structure. Current distributions of AutoDock consist...
  • VisIt

  • Referenced in 31 articles [sw05611]
  • three-dimensional (2D and 3D) structured and unstructured meshes. It was designed to interactively handle...
  • RAPTOR

  • Referenced in 19 articles [sw09002]
  • approach to do protein 3-dimensional (3D) structure prediction via threading. Based on the contact ... graph of the protein 3D structure template, the protein threading problem is formulated...
  • XFEM

  • Referenced in 358 articles [sw01026]
  • modular and extensible system. The programme structure has been designed to meet all natural requirements ... dimensions as well as complex 3D industrial problems...
  • PyMOL

  • Referenced in 38 articles [sw09662]
  • visualization product for rendering and animating 3D molecular structures...
  • FoldRate

  • Referenced in 15 articles [sw35301]
  • knowledge of their 3D (three dimensional) structures is becoming increasingly wide. It is highly desired ... however, need both the sequence and 3D structure information for predicting the folding rate...
  • iCDI-PseFpt

  • Referenced in 15 articles [sw30067]
  • knowledge of the 3D (three-dimensional) structure of protein, unfortunately their ... usage is quite limited because the 3D structures for most protein ion channels are still...
  • SnapPy

  • Referenced in 108 articles [sw06874]
  • manifolds, with a focus on hyperbolic structures. It runs on Mac OS X, Linux ... Windows, and combines a link editor and 3D-graphics for Dirichlet domains and cusp neighborhoods...
  • I-TASSER

  • Referenced in 17 articles [sw17207]
  • function prediction based on the sequence-to-structure-to-function paradigm. Starting from an amino ... three-dimensional (3D) atomic models from multiple threading alignments and iterative structural assembly simulations ... protein is then inferred by structurally matching the 3D models with other known proteins ... contains full-length secondary and tertiary structure predictions, and functional annotations on ligand-binding sites...
  • Rate4Site

  • Referenced in 7 articles [sw35756]
  • proteins of known three-dimensional (3D) structure exist, with yet unknown function. In light ... recent progress in structure determination methodology, this number is likely to increase rapidly. A novel ... homologues whose 3D-structure is known. Functionally important regions often correspond to surface patches...
  • OpenLB

  • Referenced in 15 articles [sw08549]
  • second audience, the structure of the code is kept conceptually simple, implementing basic concepts ... single generic code for various 3D lattice structures, such as D3Q15, D3Q19, and D3Q27...
  • SWISS-MODEL

  • Referenced in 14 articles [sw17373]
  • automated comparative modeling of three-dimensional (3D) protein structures. It pioneered the field of automated ... server computed 120 000 user requests for 3D protein models. SWISS-MODEL provides several levels ... protein is submitted to build a 3D model. Template selection, alignment and model building ... DeepView (Swiss-PdbViewer), an integrated sequence-to-structure workbench. All models are sent back...
  • Netgen

  • Referenced in 156 articles [sw06679]
  • Solid Geometry (CSG). The whole task of 3D mesh generation splits into four subproblems ... method. Emphasis is given to the abstract structure of the element generation rules. Several techniques...
  • ARTS

  • Referenced in 6 articles [sw13836]
  • aligning a pair of nucleic acid 3D structures (RNAs or DNAs) and detecting a-priori ... used to search 3D databases given a query structure. Recently, ARTS was used to construct ... classification database of all solved RNA 3D structures...
  • FoldX

  • Referenced in 9 articles [sw21771]
  • macromolecule based on its high-resolution 3D structure, is now publicly available through...
  • Jmol

  • Referenced in 13 articles [sw15016]
  • open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials...