• PSICO

  • Referenced in 10 articles [sw10910]
  • protein structures with constraint programming and optimization. In this paper we propose PSICO (Processing Structural ... constraint-based approach to determining protein structures compatible with distance constraints obtained from Nuclear Magnetic...
  • iBP

  • Referenced in 7 articles [sw30618]
  • Tuning interval branch-and-prune for protein structure determination. The interval branch and prune ... tractable general-purpose alternative to existing structure determination algorithms. This work introduces an iterative variant ... algorithm that leverages existing knowledge of protein structures in order to reduce the size...
  • VADAR

  • Referenced in 6 articles [sw12496]
  • graphs for quantitatively and qualitatively assessing protein structures determined by X-ray crystallography, NMR spectroscopy...
  • DISCO

  • Referenced in 7 articles [sw13152]
  • applied to the problem of determining protein moleculer structure. Tests are performed on molecules taken...
  • PICKY

  • Referenced in 4 articles [sw35293]
  • unsolved problem for automated NMR protein structure determination. Such a process is a prerequisite ... overhauser enhancement (NOE) distance restraint assignment, and structure calculation tasks. Manual or semi-automatic peak ... spectra of eight target proteins, and achieves an average of 88% recall and 74% precision...
  • Situs

  • Referenced in 4 articles [sw09515]
  • Situs: A Package for Docking Crystal Structures into Low-Resolution Maps from Electron Microscopy. Three ... image reconstructions of large-scale protein aggregates are routinely determined by electron microscopy ... data with high-resolution structures of proteins determined by x-ray crystallography ... robust method for the localization of protein subunits in low-resolution data. Topology-representing neural...
  • MULTICOM

  • Referenced in 2 articles [sw15827]
  • these proteins (e.g.  90,000) have known tertiary structures determined by experimental techniques ... determination techniques. Computational tools of predicting the structure and structural features of a protein...
  • CCP4

  • Referenced in 7 articles [sw22910]
  • programs that allows researchers to determine macromolecular structures by X-ray crystallography, and other biophysical ... edge approaches to experimental determination and analysis of protein structure, and integrate these approaches into...
  • PDB-REPRDB

  • Referenced in 5 articles [sw26865]
  • increased rapidly with determination of numbers of membrane protein structures because of improved...
  • QMEAN

  • Referenced in 7 articles [sw17377]
  • component of protein structure prediction, since ultimately the accuracy of a model determines its usefulness ... specific applications. Usually, in the course of protein structure prediction a set of alternative models...
  • PREvaIL

  • Referenced in 10 articles [sw25073]
  • using sequence, structural, and network features in a machine-learning framework. Determining the catalytic residues ... understanding the relationship between protein sequence, structure, function, and enhancing our ability to design novel ... sequenced, and their primary and tertiary structures determined, experimental methods for enzyme functional characterization ... both understanding the complex sequence-structure-function relationships of proteins and facilitating the characterization...
  • Rate4Site

  • Referenced in 7 articles [sw35756]
  • determinants within their homologues. Motivation: A number of proteins of known three-dimensional (3D) structure ... light of the recent progress in structure determination methodology, this number is likely to increase ... homologous proteins onto the molecular surface of one of the homologues whose 3D-structure...
  • PreDisorder

  • Referenced in 2 articles [sw16902]
  • disorder prediction is important for protein structure prediction, structure determination and function annotation. Results: This ... Critical Assessment of Techniques for Protein Structure Prediction (CASP8). We systematically benchmarked PreDisorder along with...
  • CANDID

  • Referenced in 1 article [sw22246]
  • Protein NMR structure determination with automated NOE assignment using the new software CANDID ... software for efficient NMR structure determination of proteins by automated assignment of the NOESY spectra ... cross-peak assignment and protein structure calculation using the fast DYANA torsion angle dynamics algorithm...
  • ElNemo

  • Referenced in 1 article [sw22480]
  • field of NMA is related to protein structure determination by X-ray crystallography, where normal ... proteins that can be treated. Upon input of a protein structure in Protein Data Bank...
  • PFRES

  • Referenced in 6 articles [sw26875]
  • prediction methods behave well when a homologous structure is predicted, but give poorer results when ... proteins that share twilight-zone sequence identity can form similar folds. Therefore, determination of structural ... RESULTS: The proposed PFRES method for automated protein fold classification from low identity (<35%) sequences...
  • SCPRED

  • Referenced in 6 articles [sw26876]
  • Background: Protein structure prediction methods provide accurate results when a homologous protein is predicted, while ... thus determining structural similarity without the sequence similarity would be desirable for the structure prediction ... folding type of a protein or its domain is defined as the structural class. Current...
  • PRODIGY

  • Referenced in 1 article [sw34227]
  • Summary: Gaining insights into the structural determinants of proteinprotein interactions holds ... strength for a given proteinprotein complex. Here we present PROtein binDIng enerGY prediction (PRODIGY ... binding affinity of proteinprotein complexes from their 3D structure. The PRODIGY server implements...
  • bamboo

  • Referenced in 2 articles [sw26313]
  • Bayesian model of protein primary sequence for secondary structure prediction. Determining the primary structure ... knob-socket model of protein packing in secondary structure. The method considers the packing ... influence of residues on the secondary structure determination, including those packed close in space...
  • WaveSpect0

  • Referenced in 4 articles [sw08760]
  • Proteomics aims at determining the structure, function and expression of proteins. High-throughput mass spectrometry...