• MIBPB

  • Referenced in 51 articles [sw08106]
  • biomolecule and the solvent. For protein molecular surfaces, which may possess troublesome geometrical singularities...
  • TMSmesh

  • Referenced in 19 articles [sw14719]
  • TMSmesh: A Robust Method for Molecular Surface Mesh Generation Using a Trace Technique. Qualified, stable ... efficient molecular surface meshing appears to be necessitated by recent developments for realistic mathematical modeling ... present a new method: tracing molecular surface for meshing (TMSmesh) the Gaussian surface of biomolecules ... existing methods for surface generation used in molecular visualization and geometry analysis. Moreover, the meshes...
  • TABI

  • Referenced in 22 articles [sw18194]
  • normal derivative on the molecular surface. The surface is triangulated and the integral equations ... uniform clusters adapted to the molecular surface. For the protein test case, we compare TABI...
  • CGAL

  • Referenced in 374 articles [sw00118]
  • aided design and modeling, geographic information systems, molecular biology, medical imaging, robotics and motion planning ... generation (2D Delaunay mesh generation and 3D surface and volume mesh generation, skin surfaces), geometry...
  • Rate4Site

  • Referenced in 7 articles [sw35756]
  • identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues ... evolution among homologous proteins onto the molecular surface of one of the homologues whose...
  • TexMol

  • Referenced in 5 articles [sw13086]
  • potential) to be mapped onto the molecular surface, tying molecular structure to molecular function. Finally...
  • MetaMol

  • Referenced in 3 articles [sw21777]
  • molecular skin surface. Modeling and visualizing molecular surfaces is an important and challenging task ... bioinformatics. Such surfaces play an essential role in better understanding the chemical and physical properties ... molecules. However, constructing and displaying molecular surfaces requires complex algorithms. In this article we introduce ... piecewise-defined algebraic equation of the molecular skin surface. As a result, both better performances...
  • ConSurf

  • Referenced in 5 articles [sw35754]
  • Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic Information. Summary: We recently ... Projecting the conservation grades onto the molecular surface of these proteins reveals patches of highly...
  • SURFNET

  • Referenced in 3 articles [sw12497]
  • SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions. The SURFNET program generates ... molecular surfaces and gaps between surfaces from 3D coordinates supplied in a PDB-format file ... data points. All output surfaces can be viewed interactively, along with the molecules or data ... known molecular modeling packages. In addition, PostScript output is available, and the generated surfaces...
  • SIMS

  • Referenced in 2 articles [sw21778]
  • SIMS: Computation of a smooth invariant molecular surface. SIMS, a new method of calculating ... SIMS method generates the smooth molecular surface by rolling two probe spheres. A solvent probe ... molecule and produces a Richards-Connolly molecular surface (MS), which envelops the solvent-excluded volume ... produces self-intersecting parts of the molecular surface, which must be removed to obtain...
  • MCTDH

  • Referenced in 33 articles [sw14837]
  • molecular system evolving on one or several coupled electronic potential energy surfaces. MCTDH...
  • NSOL

  • Referenced in 2 articles [sw21620]
  • NSOL A numerical calculation program of molecular surface area, volume, and solvation energy. In computer ... GB/SA. In these methods, as solvent accessible surface area calculate fast, solvation energy could ... decided to develop fast algorithm for molecular surface area calculation. NSOL is a fast solvation ... energy calculation program using fast molecular surface area calculation algorithm...
  • PAFMPB

  • Referenced in 5 articles [sw16770]
  • AFMPB solver with automatic surface meshing for calculation of molecular solvation free energy. We present ... tool is embedded for automatic molecular VDW/SAS surface mesh generation, leaving the requirement...
  • EIRENE

  • Referenced in 9 articles [sw18048]
  • external databases for atomic and molecular data and for surface reflection data, and it calls...
  • TINKER

  • Referenced in 10 articles [sw04095]
  • OPLS (OPLS-UA, OPLS-AA), Merck Molecular Force Field (MMFF), Liam Dang’s polarizable model ... calculations, efficient truncated Newton (TNCG) local optimization, surface areas and volumes with derivatives, simple free ... symplectic RESPA multiple time step integration for molecular dynamics, velocity Verlet stochastic dynamics, pairwise neighbor ... Monte Carlo Minimization (MCM) for efficient potential surface scanning, and more...
  • ARVO

  • Referenced in 14 articles [sw00049]
  • Fortran package for computing the solvent accessible surface area and the excluded volume of overlapping ... energy of proteins, hydration effects, drug binding, molecular docking, etc., it is important to have ... exact algorithms for computing the solvent accessible surface area and the excluded volume of macromolecules.We...
  • GDIS

  • Referenced in 1 article [sw39399]
  • GDIS: a visualization program for molecular and periodic systems. GDIS is a freely available chemical ... mechanism for constructing and manipulating arbitrary crystal surfaces. This enables GDIS to offer a powerful ... tool set for computing surface and interfacial properties and predicting crystal morphologies. Also included ... computing powder diffraction patterns, generating molecular surfaces, and analyzing dynamics trajectories. Further, the program...
  • MolSurfComp

  • Referenced in 1 article [sw32951]
  • MolSurfComp is a Matlab package for molecular surface computation, in particular, for the solvent excluded...
  • GFIT3C

  • Referenced in 2 articles [sw10213]
  • program GFIT3C which computes potential energy surfaces for molecular systems that fit at initio data...
  • GFIT4C

  • Referenced in 3 articles [sw10211]
  • Global potential energy surfaces (GPES) for tetratomic molecular systems, containing at least one group...