• LISREL

  • Referenced in 323 articles [sw06514]
  • methods and software have become synonymous with structural equation modeling (SEM). SEM allows researchers ... social sciences, management sciences, behavioral sciences, biological sciences, educational sciences and other fields to empirically...
  • DAISY

  • Referenced in 44 articles [sw09059]
  • priori global identifiability is a structural property of biological and physiological models. It is considered ... noise-free observations and error-free model structure). Of course, determining if the parameters ... performing actual biomedical experiments. Many interesting biological models are nonlinear but identifiability analysis for nonlinear...
  • CGAL

  • Referenced in 355 articles [sw00118]
  • design and modeling, geographic information systems, molecular biology, medical imaging, robotics and motion planning, mesh ... Computational Geometry Algorithms Library (CGAL), offers data structures and algorithms like triangulations (2D constrained triangulations...
  • Lynx

  • Referenced in 10 articles [sw13643]
  • case-study from computational biology, namely, the RNA secondary structure prediction problem. The constraints that ... constraints, which describe properties of the biological structure of the solution, and energetic constraints, which...
  • LAS

  • Referenced in 18 articles [sw17180]
  • exploratory tool for the discovery of biologically relevant structures in high dimensional data. Software...
  • GlobPlot

  • Referenced in 8 articles [sw06213]
  • needed for many biochemical studies, particularly structural biology. GlobPlot has a pipeline interface—GlobPipe...
  • Pfold

  • Referenced in 12 articles [sw23813]
  • structures are important in many biological processes and efficient structure prediction can give vital directions...
  • MESSI

  • Referenced in 13 articles [sw33875]
  • structure of MESSI biological systems. We introduce a general framework for biological systems, called MESSI ... prove general results based on the network structure. Many post-translational modification networks are MESSI...
  • X-PLOR

  • Referenced in 6 articles [sw13151]
  • program system for computational structural biology. X-PLOR stands for exploration of conformational space ... stands for exploration of modern concepts of structured programming in macromolecular simulation...
  • CCP4

  • Referenced in 5 articles [sw22910]
  • training of scientists in experimental structural biology. It encourages the wide dissemination of new ideas...
  • PAUP*

  • Referenced in 51 articles [sw07834]
  • applications in areas as diverse as conservation biology, ecology, and forensic studies. The success ... permutation tests for nonrandomness of data structure. These, along with many other improvements, will make ... even more indispensable tool in comparative biological analysis than were previous editions of the program...
  • STAMP

  • Referenced in 43 articles [sw09536]
  • Structural Time Series Analyser, Modeller and Predictor. Structural time series models are formulated directly ... subjects, including economics, finance, sociology, management science, biology, geography, meteorology and engineering. STAMP bridges ... providing the necessary tool to make interactive structural time series modelling available for empirical work...
  • SBL

  • Referenced in 4 articles [sw34124]
  • Template C++/Python library for solving structural biology problems. The SBL provides programs (executables...
  • VMD

  • Referenced in 83 articles [sw18651]
  • designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid ... Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods...
  • Bio3d

  • Referenced in 3 articles [sw15706]
  • package bio3d: Biological Structure Analysis. Utilities to process, organize and explore protein structure, sequence ... mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal ... environment to work with biological sequence and structural data. Please refer to the URLs below...
  • GenSSI

  • Referenced in 11 articles [sw10712]
  • GenSSI: a software toolbox for structural identifiability analysis of biological models. Mathematical modeling ... role in systems biology. Model building is often regarded as an iterative loop involving several ... often overlooked) property: the so-called structural (or a priori) identifiability, which considers the uniqueness...
  • Palingol

  • Referenced in 7 articles [sw04635]
  • DNA/RNA level, biological signals are defined by a combination of spatial structures and sequence motifs ... scanning programs are usually dedicated to particular structures and are written using general purpose programming ... consuming process where the biological problem of defining the structure and the computer engineering problem...
  • FANMOD

  • Referenced in 13 articles [sw26134]
  • concept to uncover structural design principles of complex biological networks. FANMOD is a tool...
  • StrBioLib

  • Referenced in 2 articles [sw16906]
  • library for development of custom computational structural biology applications. Summary: StrBioLib is a library ... useful for developing software for computational structural biology research. StrBioLib contains classes to represent...
  • ParCrys

  • Referenced in 3 articles [sw16920]
  • crystallization is useful in current Structural Biology efforts and in particular in high-throughput Structural...