• 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 ... general molecules, as VMD can read standard Protein Data Bank (PDB) files and display ... molecule undergoing simulation on a remote computer...
  • MEGA

  • Referenced in 34 articles [sw09078]
  • evolutionary relationships and patterns of DNA and protein evolution. In addition to the tools ... distance matrices. Here we discuss the motivation, design principles and priorities that have shaped ... analyze large data set using new computational methods...
  • GOLEM

  • Referenced in 52 articles [sw24695]
  • problems such as protein structure prediction and finite element mesh design. GOLEM copes efficiently with ... selects several pairs of positive examples and computes their rlggs. Among these rlggs, GOLEM chooses...
  • Osprey

  • Referenced in 3 articles [sw21400]
  • globally optimal protein design search, guaranteeing that the computational predictions are optimal with respect ... describe OSPREY, a protein redesign suite that implements our protein design algorithms. OSPREY has been...
  • HMMER

  • Referenced in 18 articles [sw10514]
  • searching. HMMER is a software suite for protein sequence similarity searches using probabilistic methods. Previously ... mainly been available only as a computationally intensive UNIX command-line tool, restricting ... hmmer.janelia.org) has been designed and implemented such that most protein database searches return within...
  • MAESTRO

  • Referenced in 1 article [sw16883]
  • support basic research and protein design tasks, several computational tools for predicting the change ... changes in stability upon point mutation in proteins called MAESTRO. MAESTRO is structure based...
  • STRING

  • Referenced in 28 articles [sw23938]
  • desirable, including lower-quality data and/or computational predictions. The STRING database (http://string-db.org/) aims ... scored and integrated, resulting in comprehensive protein networks covering >1100 organisms. Here, we describe ... full-text articles; (ii) we entirely re-designed the algorithm for transferring interactions from...
  • Osprey

  • Referenced in 1 article [sw29016]
  • optimization of machine learning algorithms. It’s designed to provide a practical, easy ... primary application areas in computational protein dynamics and drug design, and distributed under the Apache...
  • pLoc-mVirus

  • Referenced in 24 articles [sw24439]
  • highly demanded to develop computational tools for timely annotating their subcellular locations based ... current study is focused on virus proteins. Although considerable efforts have been made in this ... deal with single-location proteins only. Actually, proteins with multi-locations may have some special ... multiplex proteins is particularly important for both basic research and drug design. Using the multi...
  • pLoc-mGneg

  • Referenced in 23 articles [sw25190]
  • highly desired to develop computational tools for timely identifying their subcellular locations based ... Gram-negative bacterial proteins. Although considerable efforts have been made in protein subcellular prediction ... have indicated that many Gram-negative bacterial proteins exist in two or more location sites ... deal with single-location proteins only. Actually, proteins with multi-locations may have some special...
  • MSAProbs

  • Referenced in 3 articles [sw12007]
  • multiple sequence alignment have been designed, the efficient computation of highly accurate multiple alignments ... practical multiple alignment algorithm for protein sequences. The design of MSAProbs is based...
  • Fu-SulfPred

  • Referenced in 3 articles [sw36890]
  • sulfenylation sites. However, the performance of identifying protein S-sulfenylation sites can be influenced ... application of various computational methods. In this study, we designed a Fu-SulfPred model using ... decision trees in order to identify possible protein S-sulfenylation sites by means of reconstructing...
  • PREvaIL

  • Referenced in 10 articles [sw25073]
  • relationship between protein sequence, structure, function, and enhancing our ability to design novel enzymes ... catalytic residues are resource- and labor-intensive, computational approaches have considerable value and are highly ... this study, we describe a new computational method called PREvaIL for predicting enzyme catalytic residues ... complex sequence-structure-function relationships of proteins and facilitating the characterization of novel enzymes lacking...
  • GeneScout

  • Referenced in 7 articles [sw31815]
  • contains specially designed hidden Markov models (HMMs) for detecting functional sites including protein-translation start ... also proposed for exon coding potential computation. Our main hypothesis is that, given a vertebrate...
  • ProtNet

  • Referenced in 1 article [sw29365]
  • designed and implemented a computer model that captures the discrete and stochastic nature of protein...
  • SCPRED

  • Referenced in 6 articles [sw26876]
  • structure prediction. The folding type of a protein or its domain is defined ... designed features as its input to predict the structural classes. Based on extensive design that ... feature computed from the sequence. Tests performed with datasets of 1673 protein chains, in which ... achieved by SCPRED is attributed to the design of the features, which are capable...
  • TABASCO

  • Referenced in 2 articles [sw20856]
  • elongation, termination, and interactions of polymerases and proteins, Tabasco automatically traverses the state ... simulation at such high resolution computationally feasible. Tabasco was designed to allow us to better ... those interested in explicitly simulating hypotheses of protein-DNA interactions and their relation to gene...
  • BetaSCP2

  • Referenced in 1 article [sw09840]
  • computational cornerstones for many important problems such as protein design, flexible docking of proteins, homology...
  • ACEMD

  • Referenced in 7 articles [sw21783]
  • engine supporting CHARMM and AMBER force fields. Designed specifically for GPUs it is able ... performance of 40 ns/day for all-atom protein systems with over 23 000 atoms ... explicit TIP3P water on a single workstation computer equipped with just 3 GPUs. We believe...
  • MC73

  • Referenced in 7 articles [sw12394]
  • graph partitioning, protein analysis, data mining, machine learning, and web search. The computation ... novel and efficient parallel algorithm for computing the Fiedler vector of large graphs based ... method with a multilevel scheme, designed specifically for computing the Fiedler vector, which is implemented...