• Jmol

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

  • Referenced in 8 articles [sw04049]
  • similarity.In an MDL Molfile (.mdl) the 3D-structure of a molecule can be described...
  • MATRAS

  • Referenced in 4 articles [sw16871]
  • MATRAS: a program for protein 3D structure comparison. The recent accumulation of large amounts ... 3D structural data warrants a sensitive and automatic method to compare and classify these structures ... server for comparing protein 3D structures using the program Matras (http://biunit.aist-nara.ac.jp/matras). An advantage ... useful tools for insights into protein 3D structures...
  • iPfam

  • Referenced in 8 articles [sw29349]
  • Pfam domain interactions based on known 3D structures that are found in the Protein Data...
  • iPARTS

  • Referenced in 4 articles [sw13839]
  • server for aligning two RNA 3D structures based on a structural alphabet (SA)-based approach ... this SA to transform RNA 3D structures into 1D sequences of SA letters and continue ... iPARTS takes as input two RNA 3D structures in the PDB format and outputs their ... enlarge the superposition of aligned RNA 3D structures. iPARTS is now available online...
  • FastImp

  • Referenced in 5 articles [sw13145]
  • EMQS) and fullwave analysis of complicated 3D structures from zero frequency to at least tens ... Giga Hertz. These 3D structures are commonly seen in interconnects and packages of VLSI circuits...
  • HHpred

  • Referenced in 7 articles [sw17271]
  • local or global alignment and scoring secondary structure similarity. HHpred can produce pairwise query-template ... search results, as well as 3D structural models that are calculated by the MODELLER software...
  • DIAL

  • Referenced in 6 articles [sw13837]
  • pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing ... dynamic programming algorithm for pairwise 3D structural alignment of RNA. DIAL achieves quadratic time ... used to detect structurally similar occurrences of a user-specified 3D motif. The query motif...
  • OptiStruct

  • Referenced in 13 articles [sw14224]
  • engineers rapidly develop innovative, lightweight and structurally efficient designs. Continuing to build ... design and optimization of 3D printed lattice structures and advanced materials such as laminate composites...
  • FRANC3D

  • Referenced in 4 articles [sw09492]
  • representing the geometry and topology of 3D structures with arbitrary non-planar cracks, along with ... functionality for 1) discretizing or meshing the structure, 2) attaching boundary conditions at the geometry ... windows for the display of the 3D structure and a menu and dialog-box system ... either surface or volume meshes. Consequently, any 3D boundary or finite element program, capable...
  • SARSA

  • Referenced in 4 articles [sw13834]
  • conformations, via which we transform RNA 3D structures into 1D sequences of SA letters ... structural similarity, (ii) semiglobal alignment for detecting structural motifs, (iii) local alignment for finding locally ... SARSA take as input RNA 3D structures in the PDB format and in their outputs...
  • NNcon

  • Referenced in 6 articles [sw17013]
  • folding rate prediction, model selection and 3D structure prediction. Here we describe NNcon, a fast...
  • SPECFEM3D

  • Referenced in 6 articles [sw09304]
  • Earth. These waves help reveal the 3D structure of the Earth’s deep interior...
  • CHARMS

  • Referenced in 36 articles [sw02957]
  • independent of domain dimension (here 2D and 3D), element type (e.g., triangle, quad, tetrahedron, hexahedron ... structure support. We demonstrate the versatility of our new approach through 2D and 3D examples...
  • PointNet

  • Referenced in 25 articles [sw31209]
  • 3D Classification and Segmentation. Point cloud is an important type of geometric data structure...
  • TetGen

  • Referenced in 156 articles [sw04046]
  • correctness. It can robustly handle arbitrary complex 3D geometries and is fast in practice ... TetGen, including an efficient tetrahedral mesh data structure, a set of enhanced local mesh operations...
  • ACD/ChemSketch

  • Referenced in 5 articles [sw36954]
  • structures including organics, organometallics, polymers, and Markush structures. It also includes features such as calculation ... density, molar refractivity etc.), 2D and 3D structure cleaning and viewing, functionality for naming structures...
  • FR3D

  • Referenced in 5 articles [sw13838]
  • toward the end of the RNA 3D structure course materials at this link. WebFR3D...
  • FEKO

  • Referenced in 5 articles [sw18219]
  • electromagnetic field analysis of 3D structures. It offers multiple state-of-the-art numerical methods...
  • ESyPred3D

  • Referenced in 5 articles [sw16876]
  • ESyPred3D: Prediction of proteins 3D structures. Motivation: Homology or comparative modeling is currently the most...