• ARVO

  • Referenced in 14 articles [sw00049]
  • Fortran package for computing the solvent accessible surface area and the excluded volume of overlapping ... exact algorithms for computing the solvent accessible surface area and the excluded volume of macromolecules.We...
  • FreeSASA

  • Referenced in 3 articles [sw21619]
  • open source C library for solvent accessible surface area calculations. Calculating solvent accessible surface areas...
  • NSOL

  • Referenced in 2 articles [sw21620]
  • numerical calculation program of molecular surface area, volume, and solvation energy. In computer simulation ... that calculate solvation energy using solvent accessible surface area; ASP (atomic solvation parameters) model ... GB/SA. In these methods, as solvent accessible surface area calculate fast, solvation energy could...
  • SPIDER2

  • Referenced in 2 articles [sw25872]
  • predicted properties are secondary structure and accessible surface area (ASA) representing local and nonlocal structural ... coefficient between predicted and actual solvent accessible surface area, 19° and 30° for mean absolute ... prediction of local structure and solvent accessible surface area. The method is implemented...
  • Naccess

  • Referenced in 8 articles [sw12485]
  • naccess 2.1.1 Atomic Solvent Accessible Area Calculation Software: Developed at UCL by Simon Hubbard ... Thornton, this program calculates absolute and relative surface accessibilities of protein and nucleic acid structures...
  • ASAView

  • Referenced in 3 articles [sw35659]
  • solvent accessibility provides a convenient graphical view of residues in terms of their exposed surface ... areas. In addition, sequential plots in the form of bar charts are also provided. Online ... separately. Conclusions: These graphical plots of solvent accessibility are likely to provide a quick view...
  • RSARF

  • Referenced in 5 articles [sw22442]
  • accurate structure prediction. Knowledge of residue solvent accessibility gives useful insights into protein structure prediction ... forest method, RSARF, to predict residue accessible surface area from protein sequence information. The training ... useful for prediction of residue solvent accessibility from protein sequence without using structural information...
  • HSEpred

  • Referenced in 3 articles [sw25088]
  • newly developed two-dimensional solvent exposure measure. By conceptually separating an amino acid’s sphere ... compared with other measures such as accessible surface area, residue depth and contact number. However...
  • Prodepth

  • Referenced in 0 articles [sw25085]
  • solvent exposure measure that complements the information provided by conventional accessible surface area...
  • hypre

  • Referenced in 263 articles [sw00426]
  • hypre is a software library for the solution...
  • LAPACK

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

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

  • Referenced in 54 articles [sw01333]
  • AmberTools is a set of programs for biomolecular...
  • LIBSVM

  • Referenced in 1088 articles [sw04879]
  • LIBSVM is a library for Support Vector Machines...
  • PyMOL

  • Referenced in 38 articles [sw09662]
  • PyMOL is a powerful and comprehensive molecular visualization...
  • VARNA

  • Referenced in 5 articles [sw16406]
  • VARNA: Interactive drawing and editing of the RNA...
  • MINT

  • Referenced in 1 article [sw16407]
  • MINT: software to identify motifs and short-range...