• MEIGO

  • Referenced in 6 articles [sw08492]
  • solve many problems in computational biology. Global optimization methods provide a robust methodology, and metaheuristics...
  • VMD

  • Referenced in 84 articles [sw18651]
  • graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows ... designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid ... molecule undergoing simulation on a remote computer...
  • ADAM

  • Referenced in 8 articles [sw21957]
  • analysis of discrete models of biological systems using computer algebra. BACKGROUND: Many biological systems ... gain a better understanding of them. The computational complexity to analyze the complete dynamics ... computer algebra. Based on extensive experimentation with both discrete models arising in systems biology...
  • BLAD

  • Referenced in 19 articles [sw08612]
  • Differential elimination and biological modelling. This paper describes applications of a computer algebra method, differential ... applied mathematics problems mostly borrowed from biology. The two considered applications are related to parameter ... package, which is embedded in the MAPLE computer algebra software, and the BLAD libraries which...
  • PESTO

  • Referenced in 6 articles [sw28243]
  • PESTO has been used in various computational biology research projects. PESTO features include: Multistart optimization...
  • BioStream

  • Referenced in 4 articles [sw07745]
  • orchestrating the reactions needed in a biological computer. Thousands of microfluidic primitives have already been ... presents BioStream, a portable language for describing biology protocols, and the Fluidic ISA, a stable ... important step towards building scalable biological computers...
  • SEGM

  • Referenced in 5 articles [sw30070]
  • server is to date the only computational biology software in this evolutionary approach...
  • Spikenet

  • Referenced in 12 articles [sw08892]
  • biological neural network models face the problem of scalability because of the limited computational power ... modelled. We describe the underlying computation and implementation of such a mechanism in SpikeNET ... build is not only biologically compliant, it is also computationally efficient as 400 000 synaptic...
  • Cell-PLoc

  • Referenced in 90 articles [sw09126]
  • interesting, because they may have some special biological functions intriguing to investigators in both basic ... predictors in the Cell-PLoc package. The computational time for each prediction is less than...
  • SAPPER

  • Referenced in 5 articles [sw18894]
  • emergence of new applications, e.g., computational biology, new software engineering techniques, social networks, etc., more...
  • PDB-REPRDB

  • Referenced in 5 articles [sw26865]
  • system was moved to the Computational Biology Research Center (CBRC), National Institute of Advanced Industrial...
  • DESMOND

  • Referenced in 12 articles [sw06114]
  • speed molecular dynamics simulations of biological systems on conventional computer clusters...
  • MGS

  • Referenced in 9 articles [sw22121]
  • simulation of biological processes, especially those whose state space must be computed jointly with ... unified view on several computational mechanisms initially inspired by biological or chemical processes (Gamma ... Paun systems and cellular automata). The basic computation step in MGS replaces in a collection...
  • PAUP*

  • Referenced in 53 articles [sw07834]
  • based formats. The influence of high-speed computer analysis of molecular, morphological and/or behavioral data ... well beyond its central role in evolutionary biology, now encompassing applications in areas as diverse...
  • MCQ4Structures

  • Referenced in 4 articles [sw15705]
  • solving various problems derived from computational biology, like structure alignment and modelling, motif search ... method and tool for structural similarity computation based on molecule tertiary structure representation in torsional...
  • OPERAS

  • Referenced in 4 articles [sw30593]
  • characteristics of finite state machines and biological computation systems, such as X-machines...
  • KIRMES

  • Referenced in 4 articles [sw35269]
  • main challenges in computational biology. An important problem is the identification of transcription factor...
  • iPromoter-2L

  • Referenced in 23 articles [sw24788]
  • their importance in biological process, it is highly desired to develop computational tools for timely...
  • AQUASOL

  • Referenced in 3 articles [sw17113]
  • requirement for problems commonly encountered in computational biology and computational chemistry. To circumvent these problems...
  • X-PLOR

  • Referenced in 6 articles [sw13151]
  • PLOR is a program system for computational structural biology. X-PLOR stands for exploration...