• APBS

  • Referenced in 95 articles [sw05766]
  • ligand-protein and protein-protein binding kinetics, implicit solvent molecular dynamics of biomolecules, solvation...
  • Cell-PLoc

  • Referenced in 90 articles [sw09126]
  • more different subcellular locations. Proteins with multiple locations or dynamic features of this kind...
  • Euk-mPLoc

  • Referenced in 42 articles [sw26860]
  • bearing the multiplex feature. Proteins with multiple locations or dynamic feature of this kind ... Prot database, the number of total eukaryotic protein entries (except those annotated with ”fragment...
  • InterViewer

  • Referenced in 31 articles [sw00443]
  • InterViewer: Dynamic visualization of protein-protein interactions From the perspective of graph drawing, a protein...
  • Gromacs

  • Referenced in 124 articles [sw04128]
  • versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems ... primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have...
  • Hum-mPLoc

  • Referenced in 26 articles [sw26862]
  • more different subcellular locations. Proteins with multiple locations or dynamic feature of this kind ... discovery. For instance, among the 6408 human protein entries that have experimentally observed subcellular location...
  • iMethyl-PseAAC

  • Referenced in 21 articles [sw22443]
  • Knowledge of PTMs in proteins is crucial for dynamic proteome analysis of various human diseases ... arginine or lysine, respectively. Given a protein, which site...
  • E-CELL

  • Referenced in 23 articles [sw07917]
  • simulating intracellular molecular processes to predict the dynamic behavior of living cells. Previous work ... allows a user to define functions of proteins, protein-protein interactions, protein-DNA interactions, regulation ... through a computer display, dynamic changes in concentrations of proteins, protein complexes and other chemical...
  • BioGRID

  • Referenced in 48 articles [sw17422]
  • file formats. User-customized graphs with embedded protein, gene and interaction attributes can be constructed ... visualization system called Osprey that is dynamically linked to the BioGRID...
  • ProDy

  • Referenced in 4 articles [sw24072]
  • ProDy: protein dynamics inferred from theory and experiments. SUMMARY: We developed a Python package, ProDy ... structure-based analysis of protein dynamics. ProDy allows for quantitative characterization of structural variations ... equilibrium dynamics. Datasets include structural ensembles for a given family or subfamily of proteins, their...
  • FoldX

  • Referenced in 9 articles [sw21771]
  • mutations on the stability, folding and dynamics of proteins and nucleic acids. The core functionality...
  • iSNO-AAPair

  • Referenced in 24 articles [sw22447]
  • important and universal posttranslational modifications (PTMs) of proteins, S-nitrosylation (SNO) plays crucial roles ... cellular dynamics and many signaling events. Knowledge of SNO sites in proteins is very useful...
  • UHBD

  • Referenced in 8 articles [sw08088]
  • simulations with the University-of-Houston Brownian dynamics program. This paper is a follow ... pKas of ionizable groups in proteins, performing Brownian dynamics simulations with a flexible substrate...
  • VAMPnets

  • Referenced in 19 articles [sw32927]
  • processes, such as protein-drug binding, from high-throughput molecular dynamics simulations. Current methods employ...
  • VMD

  • Referenced in 90 articles [sw18651]
  • general molecules, as VMD can read standard Protein Data Bank (PDB) files and display ... analyze the trajectory of a molecular dynamics (MD) simulation. In particular...
  • SSAP

  • Referenced in 7 articles [sw08918]
  • automatically comparing three dimensional protein structures using double dynamic programming...
  • ENCoM

  • Referenced in 2 articles [sw16880]
  • effect of single point mutations on protein dynamics and thermostability resulting from vibrational entropy changes...
  • TM-align

  • Referenced in 15 articles [sw22248]
  • alignment between protein pairs that combines the TM-score rotation matrix and Dynamic Programming ... structure comparison of 10 515 representative protein chains from the Protein Data Bank (PDB) with...
  • ProtNet

  • Referenced in 1 article [sw29365]
  • stochastic simulations of protein interaction networks dynamics. Background: Protein interactions support cell organization and mediate ... provides no clue about the dynamic nature of protein interactions inside the cell. Results ... sort of ”discrete molecular dynamics” applied to interacting proteins in a cell. We have tested ... used to simulate the dynamics of protein interactions in the cell...
  • MDAnalysis

  • Referenced in 9 articles [sw17696]
  • temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein structures. It is written...