• iHSP-PseRAAAC

  • Referenced in 16 articles [sw25193]
  • assisting in the establishment of proper protein conformation and prevention of unwanted protein aggregation. Their...
  • iPhos-PseEvo

  • Referenced in 17 articles [sw23953]
  • body by altering the structural conformation of a protein, causing it to become activated/deactivated...
  • MAMMOTH

  • Referenced in 11 articles [sw26215]
  • structural similarity score between two proteins or two different conformations of the same protein...
  • DYANA

  • Referenced in 11 articles [sw08628]
  • Sampling of conformation space in torsion angle dynamics calculations. Torsion angle dynamics (TAD) performs molecular ... protein structures from NMR data. For this application of TAD, unbiased sampling of conformation space ... study of the sampling of conformation space in protein structure calculations with the TAD algorithm...
  • HOPE

  • Referenced in 4 articles [sw32999]
  • method uses the minimum energy conformation of one protein as a template to predict ... achieved by following a path of conformations determined by a homotopy between the potential energy ... proteins. Ensembles of solutions are produced by perturbing conformations along the path, increasing the likelihood ... results are presented for pairs of homologous proteins, where HOPE is compared to a variant...
  • SCWRL4

  • Referenced in 7 articles [sw22393]
  • Improved prediction of protein side-chain conformations with SCWRL4. SCWRL4 is based ... density and presumed conformational disorder. For a testing set of 379 proteins, 86% of chi1...
  • ENCoM

  • Referenced in 2 articles [sw16880]
  • ENCoM server: exploring protein conformational space and the effect of mutations on protein function ... layer of information was shown to improve conformational space sampling and apply for the first ... effect of single point mutations on protein dynamics and thermostability resulting from vibrational entropy changes ... well as to generate geometrically realistic conformational ensembles. The server is accessible at: http://bcb.med.usherbrooke.ca...
  • HIT

  • Referenced in 1 article [sw35512]
  • interactions can be critical to establishing protein conformation (folding) and dynamics, as well as determining ... used for analysis of individual protein conformations or to gain insight into dynamic changes...
  • FlexProt

  • Referenced in 2 articles [sw37001]
  • molecules, which may appear in different conformations. Hence, protein structural analysis requires algorithms that...
  • ElNemo

  • Referenced in 1 article [sw22480]
  • biology, such as the study of protein conformational changes upon ligand binding, membrane channel opening ... emerging field of NMA is related to protein structure determination by X-ray crystallography, where ... Upon input of a protein structure in Protein Data Bank (PDB) format, ElNémo computes ... download. If two conformations of the same (or a homologous) protein are available, ElNémo identifies...
  • MCCE2

  • Referenced in 3 articles [sw14052]
  • MCCE2: Improving protein pKa calculations with extensive side chain rotamer sampling. Multiconformation continuum electrostatics (MCCE ... explores different conformational degrees of freedom in Monte Carlo calculations of protein residue and ligand ... described. The pKas calculated with different isosteric conformers, heavy atom rotamers and proton positions, with ... group of 305 experimental pKas in 33 proteins. QUICK calculations, with rotation around...
  • RASP

  • Referenced in 2 articles [sw24067]
  • RASP: rapid modeling of protein side chain conformations. Motivation: Modeling of side chain conformations constitutes ... methods for subsequent analysis and refinement of protein structures. However, these recent efforts to enhance ... improving the speed of side chain conformation prediction, we present a RApid Side-chain Predictor...
  • PBM

  • Referenced in 1 article [sw21823]
  • analyse in various ways a protein conformation. SPHERE provides for an interactive manipulation of structures ... filling models. RIBBON creates ribbon models of proteins and allows for a limited variety...
  • iMod

  • Referenced in 4 articles [sw35118]
  • versatile tool chest to explore conformational flexibility of both protein and nucleic acid structures using ... efficient framework to conduct NMA-based conformational studies, including standard vibrational analysis, Monte-Carlo simulations...
  • iScore

  • Referenced in 1 article [sw33181]
  • protein docking models. Results: Here we present iScore, a novel approach to scoring docked conformations ... obtained using a graph representation of the proteinprotein interfaces and a measure of evolutionary ... docked conformations. This work represents the first successful demonstration of graph kernels to protein interfaces ... near-native and non-native conformations of protein complexes. Availability and implementation: The iScore code...
  • CANDID

  • Referenced in 1 article [sw22246]
  • three-dimensional protein structure represented by a bundle of conformers...
  • Macrodox

  • Referenced in 2 articles [sw08087]
  • rate of attainment of optimum docking conformations of protein-protein, protein-DNA, and other complexes ... starting from coordinate information downloaded from the Protein Data Bank. Such properties would include surrounding ... automated force-guided search of docked conformers which would avoid trapping in local energy minima...
  • LOOPER

  • Referenced in 1 article [sw17376]
  • program, LOOPER, for the prediction of protein loop conformations. The method is based ... glycine, which is sampled by four representative conformations. The initial (φ, ψ) values are determined ... protein core with loop backbone atoms only. Construction and optimization of the side-chain conformations...
  • MSMBuilder

  • Referenced in 2 articles [sw23802]
  • biomolecular dynamics such as protein folding and conformational change. MSMBuilder is named for its ability...
  • ArchPRED

  • Referenced in 2 articles [sw17375]
  • conformations. The inputs to the server are the atomic coordinates of the query protein ... candidate loops are inserted in the query protein framework where their side chains are rebuilt ... propensities. The final loop conformation is built in the protein structure and annealed...