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  1. www.ccp4.ac.uk › html › rampageRAMPAGE (CCP4: Supported Program) — CCP4 documentation

    RAMPAGE is an offshoot of RAPPER which generates a Ramachandran plot using data derived by the Richardsons and coworkers. It is recommended that it be used for this purpose in preference to PROCHECK, which is based on much older data.

  2. warwick.ac.uk › fac › sciGenerating Ramachandran (phi/psi) plots for Proteins

    A selection of programs to generate and display Ramachandran (phi/psi) plots for proteins from PDB files.

  3. link.springer.com › chapter › 10Protein Structure Analysis | SpringerLink

    May 5, 2017 · The aliphatic index of a protein (volume of a protein filled by aliphatic side chains like isoleucine, alanine, valine and leucine) denotes the thermostability of globular proteins.

  4. bip.weizmann.ac.il › toolbox › structureLSCF Bioinformatics - Protein structure - Model validation -...

    Nov 27, 2019 · Model Validation. This section includes a number of web tools and databases that may help in assessing the reliability of structural models (crystallographic, NMR, or homology based models). Uses to analyze the statistics of non-bonded interactions between different atom types.

  5. cloud.ccp4.ac.uk › manuals › html-taskrefRampage — CCP4 Cloud 1.7 documentation

    Rampage. RAMPAGE is a consequence of RAPPER which generates a Ramachandran plot by data derivative by the Richardsons and coworkers. RAPPER performs conformer modelling through sampling residue-specific phi / psi propensity tables and rotameric states with given a set of restraints.

  6. link.springer.com › protocol › 10Using RAMPAGE to Identify and Annotate Promoters in Insect ... -...

    Nov 10, 2018 · In this chapter we discuss the computational analysis of the experimental data derived from one of TSS profiling methods, RAMPAGE (RNA Annotation and Mapping of Promoters for Analysis of Gene Expression) that can be used for the precise, quantitative identification of promoters in insect genomes.

  7. swift.cmbi.umcn.nl › servers › htmlRamachandran plot

    Introduction. This server will display a Ramachandran plot, against a background of phi-psi probabilities. Methods. This server will display a coloured Ramachandran plot. Blue means helix, red means strand and green means turn and loop according to DSSP. The lines in the plot indicate prefered areas.

  8. warwick.ac.uk › fac › sciDrawing Ramachandran (phi/psi) plots for Proteins with R

    Drawing Ramachandran (phi/psi) plots for Proteins with R. These pages shows how to use R to draw a protein backbone's psi/phi torsion angles (ϕ,ψ) from a supplied file as a scatter plot overlayed on a filled contour plot showing the favoured and allowed regions, for example:

  9. www.ncbi.nlm.nih.gov › pmc › articlesDawn of a New RAMPage - PMC - National Center for Biotechnology...

    Structural determinants of RAMP function. RAMPs are single-pass transmembrane proteins that consist of an ~100 amino acid N-terminal extracellular domain (ECD) and a short ~9 amino acid C-terminal intracellular domain.

  10. saves.mbi.ucla.eduSAVESv6.0 - Structure Validation Server

    Reference: Verification of protein structures: patterns of nonbonded atomic interactions, Colovos C and Yeates TO, 1993. C++ software