• FreeFem++

  • Referenced in 1396 articles [sw01436]
  • several branches of physics such as fluid-structure interactions require interpolations of data on several ... Vista,7 ) and MacOS X (native version using OpenGL). FreeFem++ replaces the older freefem...
  • AUTO-MUTE

  • Referenced in 9 articles [sw16878]
  • residue substitutions in proteins with known native structures. Trained models classify independent mutant test sets...
  • Scilab

  • Referenced in 175 articles [sw00834]
  • programming language allowing access to advanced data structures, 2-D and 3-D graphical functions ... frequency domains. Application Development: Increase Scilab native functionalities and manage data exchanges with external tools...
  • iProt-Sub

  • Referenced in 14 articles [sw27604]
  • amino acid sequence profile, secondary structure, solvent accessibility and native disorder, which will allow...
  • IUPred

  • Referenced in 7 articles [sw16915]
  • lack a well-defined three-dimensional structure under native conditions. The IUPred server presents ... predicting short or long disordered regions and structured domains. Availability: The IUPred server is available...
  • RONN

  • Referenced in 7 articles [sw16909]
  • network technique applied to the detection of natively disordered regions in proteins. Motivation: Recent studies ... form well-defined three-dimensional structures in their native states. The study and detection ... understanding protein function and for facilitating structural analysis since disordered regions may affect solubility and/or ... pattern recognition algorithm to the detection of natively disordered regions in proteins. The results...
  • APOLLO

  • Referenced in 2 articles [sw17009]
  • CASP9 (Critical Assessment of Techniques for Protein Structure Prediction) targets, the predicted quality scores generated ... with the actual distances to native structure. Availability: http://sysbio.rnet.missouri.edu/apollo/. Single and pair-wise...
  • ParTopS

  • Referenced in 4 articles [sw08857]
  • adjacency-based serial topological data structure, which can natively handle the representation of cohesive elements...
  • SMOQ

  • Referenced in 1 article [sw20299]
  • protein structural model before its native structure is known. The method that can predict ... feature set), including amino acid sequence, secondary structures, solvent accessibilities, and residue-residue contacts ... improve the performance when real deviations between native and model are higher than...
  • eXist

  • Referenced in 16 articles [sw01467]
  • existing tools and covers most of the native XML database features. An enhanced indexing scheme ... architecture’s core supports quick identification of structural node relationships. Based on this scheme...
  • Prodock

  • Referenced in 1 article [sw33075]
  • distinguishing low‐energy nonnative conformations from native structures. To make the Monte Carlo minimization method...
  • DNdisorder

  • Referenced in 3 articles [sw16907]
  • adopt a stable tertiary structure in their native state. Such regions known as disordered regions...
  • PSICOV

  • Referenced in 7 articles [sw17010]
  • PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments ... native fold of a protein, remains an open problem in the field of structural bioinformatics...
  • 3DRobot

  • Referenced in 0 articles [sw34254]
  • packed protein structure decoys. Given a native structure as input, 3DRobot first identifies diverse structure...
  • MOCCA

  • Referenced in 4 articles [sw12932]
  • pluglets, both in structure and invocation methodology. An outline of how native CCA modules...
  • SOSlib

  • Referenced in 5 articles [sw29331]
  • systems. The native API provides fine-grained interfaces to all internal data structures, symbolic operations...
  • TUNE

  • Referenced in 1 article [sw35757]
  • tested on discrimination of native and decoy protein 3D structures. With a residue level structural...
  • PGAPack

  • Referenced in 16 articles [sw04922]
  • PGAPack is a general-purpose, data-structure-neutral parallel GENETIC ALGORITHM library. It is intended ... Binary-, integer-, and real- and character-valued native data types Full extensibility to support custom...
  • AMReX

  • Referenced in 15 articles [sw23792]
  • software framework for building massively parallel block-structured AMR applications. Cell-centered, face-centered ... visualization is included; AMReX’s native format is supported by tools such as Visit, Paraview ... framework is supported by the ECP Block-Structured AMR Co-Design Center and began...
  • Kokkos

  • Referenced in 28 articles [sw20455]
  • hardware load and store operations. Such data structures are used in LAMMPS to store atom ... package supports running on the Phi in native mode, not offload mode like the USER...