User:Wayne Decatur/Structure analysis tools

From Proteopedia

• Superpose from the University of Alberta -a protein superposition server, see detailed coverage on Proteopedia about SuperPose here in relation to other structural alignment tools/servers.
• TM-align -a protein superposition/ structural alignment tool/server from the Zhang lab at the University of Michigan. "TM-align: Quick & Accurate Structural Alignment. TM-align is an algorithm for sequence independent protein structure comparisons. For two protein structures of unknown equivalence,...", see detailed coverage on Proteopedia about TM-align here in relation to other structural alignment tools/servers.
• PrePPI: database of predicted and experimentally determined protein-protein interactions (PPIs) for yeast and human.
• XtalPred - Prediction of Protein Crystallizability (program described by (this paper by Mizianty et al. entitled "Covering complete proteomes with X-ray structures: a current snapshot."^[1], supposed to be better but I couldn't find a link to a webserver running it. Or anything of it online yet.)
• PV - JavaScript Protein Viewer
• BioPandas - "Working with molecular structures in pandas DataFrames". Combining Python, Pandas, and Structural data awesomely. Has nice PDB parser that lets you get whole header, for example see [here].
• ProDy Project - "ProDy is a free and open-source Python package for protein structural dynamics analysis". Looks like it does protein sequence analysis too and working with PDB files.
• ProteinsPlus - a comprehensive collection of web-based molecular modeling tools. Associated article.

Nucleic acid in general

• Curves+ is a revised version of the Curves approach for analyzing the structure of nucleic acids. The webserver form can be accessed here where citations of the related articles are in another tab. There seems to be a command line-based one in Fortran available here.

• Despite what the name original stood for, DSSR handles nucleic acids in general as well. See the description below for links.

RNA specific

• RNArtist RNA Gallery - Precomputed 2-dimensional drawings for RNA structures stored in databases.
• DSSR -(Dissecting the Spatial Structure of RNA), an integrated and automated tool for analyzing and annotating RNA tertiary structures. PMID: 26184874 ^[2] (Maybe name of given supplemental data file previously DSSR stood for "DSSR_ a software program for Defining the Secondary Structures of RNA from three-dimensional coordinates".? Jmol now has integrated real time updates to data generated by DSSR, see here and a 2017 article on it here^[3].
• RNApdbee -a webserver to derive secondary structures from PDB files of knotted and unknotted RNAs PMID: 24771339^[4]. Use it here.
• RNArtist - allows designing of RNA 2D structures interactively. To help you to be an RNArtist, this tool provides numerous graphical options to find your theme and to modify the 2D layout.
• RNA-tools - "rna-tools is a core library and a set of programs to run various Python functions related to work, initially, with PDB files of RNA structures, but right now this is a huge toolbox of tools to process various types of RNA data."

Mutations

• SNPViz - Visualization of SNPs in proteins

Missing Residues

• FirstGlance in Jmol offers a detailed report on the numbers and properties of parts of chains not observed in a structure. Open your favorite molecule in FirstGlance in Jmol and then click on the 'Missing Residues' link on the first page that opens, under `Asymmetric Unit` section.
• Biopython can use REMARK 465 lines to parse missing residues, see my notebook `Using Biopython PDB Header Parser to get missing residues.ipynb` in my cl_demo-binder repo ( nicely rendered static version of that notebook). Also see here and here.
• article associated with it: SEQATOMS Brandt, B.W., Heringa, J. and Leunissen, J.A.M. (2008). SEQATOMS: a web tool for identifying missing regions in PDB in sequence context. Nucleic Acids Research 36:W255-W259 (It seems it just really produces data where missing is lower case? Is it run often so that the current data for current structures is available?) page at http://www.bioinformatics.nl/tools/seqatoms/
• MUFOLD-DB: a processed protein structure database for protein structure prediction and analysis.He Z, Zhang C, Xu Y, Zeng S, Zhang J, Xu D.BMC Genomics. 2014;15 Suppl 11(Suppl 11):S2. doi: 10.1186/1471-2164-15-S11-S2. Epub 2014 Dec 16. ^[5] <-- this database says it summarizes missing residues but again, I can get this from the PDB header already with `Using Biopython PDB Header Parser to get missing residues.ipynb` in my cl_demo-binder repo( nicely rendered static version of that notebook).
• Missing strings of residues in protein crystal structures. Djinovic-Carugo K, Carugo O.Intrinsically Disord Proteins. 2015 Oct 23;3(1):e1095697. doi: 10.1080/21690707.2015.1095697. eCollection 2015.^[6]
• Resolving the ambiguity: Making sense of intrinsic disorder when PDB structures disagree. DeForte S, Uversky VN.Protein Sci. 2016 Mar;25(3):676-88. doi: 10.1002/pro.2864. Epub 2016 Jan 9. ^[7]
• see 'Compare Related Structures in regards to portions not resolved' section below

Compare Related Structures in regards to portions not resolved

• • work-in-progress effort to make it easier to make summary tables of part of chains not resolved in related solved macromolecular complexes.

Compare Related Structures Protein-Protein Interaction Pairs

• Collection of notebooks to analyze PDBsum-derived data using Jupyter/Python - currently the most prominent feature here facilitates highlighting differences and similarities in protein-protein interaction of the same protein pairs in different, related macromolecular complexes. For example, structures solved with different ligands or substrates or structures that share subsets of the same components.
• PDBsum-utilities - where I share my code to analyze PDBsum-derived data using Python.

Compare Related Structures Protein-Protein or Protein-nucleic Interaction Pairs

• PDBePISA-utilities - where I share my code to analyze PDBePISA-derived data using Python.

Python-based utilities

• BioPandas - "Working with molecular structures in pandas DataFrames". Combining Python, Pandas, and Structural data awesomely. Has nice PDB parser that lets you get whole header, for example see [here].
• Gemmi - is a library for parsing PDB, cif, mtz files, and has Python bindings
• Use PyMOL via the command line in your browser in a Jupyter session by clicking `launch binder` here. A series of demonstrations of using PyMOL in the manner are included.
• seqmagick-An imagemagick-like frontend to Biopython SeqIO. For example, it can convert from fasta to phylip, remove gaps from a fasta-formatted sequence, and describe all FASTA files in the current directory. Requires Biopython.
• see also on this page 'Binder'/notebook-related items as I usually have worked out Python code to shuttle other command-line based software output to Python or demonstrate the scripts use
• click `launch binder` here for a series of demonstrations of useful resources on command line for manipulating structure files.
• PDBsum-utilities - where I share my code to analyze PDBsum-derived data using Python.
• pdbsum-binder - working with data from PDBsum integrated with Jupyter/Python
• jupyter-jsmol-binder - JMol Jsmol applets in Jupyter notebook
• Jupyter-desktop_with_pymol - PyMOL graphical user interface served via MyBinder.org
• pymol-binder - PyMOL running headless for command line/scripting and interaction with Python.
• modelit-binder - Model.it software to produce a 3D model of DNA in bent confirmation combined with Jupyter ecosystem and PyMOL served via MyBinder.org
• AnimatePymolWithJmol - Easily animate PyMOL session scenes with Jmol to create an animated GIFs

R-based utilities

• Bio3D (an R library) example along with Bio3D Python in same Jupyter notebook examples

My own structure work-related code

• Structure/model manipulation Python code
• see also on this page 'Binder'/notebook-related items as I usually have worked out Python code to shuttle other command-line based software output to Python or demonstrate the scripts use
• click `launch binder` here for a series of demonstrations of useful resources on command line for manipulating structure files.
• see 'Compare Related Structures in regards to portions not resolved' section below
• My pymol-binder adds some of my own code in for handling structures via PyMOL.

Jmol/Jsmol use in Jupyter environments

• jupyter-jsmol-binder - My current resource consolidating my efforts to use Jsmol applets in Jupyter and to take advantage of a Jupyter extension made by others to also do that. Jsmol applets directly used in Jupyter are shown here; you can run that notebook actively inside the jupyter-jsmol-binder.

Related

• User:Wayne Decatur/I-Ppo Morph Methods - uses several structure analysis tools to generate a morph of a protein-nucleic acid complex
• S. cerevisiae complexes

References

See Also

• Structural alignment tools
• Modeling
• Molecular modeling and visualization software
• User:Wayne Decatur/Code for Molecular Structure and Visualization Work