Ultimate List of Crystallography Related Programs

Apr 18, 2010

The list contains 250+ programs, databases and servers so if you are searching for a crystallography related program then there is a good chance you will find it here. If you notice a program that is missing or an update, feel free to leave a comment.


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 DNA

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 Transform Simple and easy to use program for the manipulation of sequences

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 EnzymeX Restriction enzyme information, DNA sequence editor and more (Mac)

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 Amplify Simulating and testing PCRs – designing primers by evaluating candidates

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 AMIGOS Compare RNA structures and search for specific RNA (sub)structures

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 3DNA Analysis, Rebuilding, and Visualization of 3D Nucleic Acid Structures

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 Curves+ Calculates a helical parameter description for any irregular nucleic acid segment with respect to an optimal, global helical axis – includes are the helper programs Canal, Cdif and Sumr.

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 FinchTV View and edit your DNA sequencer chromatogram data.

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 Madbend Calculates DNA, DNA-protein step roll, tilt and twist values, and the specification of a reference plane

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 Staden DNA sequence assembly, editing and analyzing tools.

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 Sequence Tools

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 Aline Format sequence alignment formats

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 Alscript Format multiple sequence alignments in PostScript for publication

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 BLAST Sequence comparision

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 ProtSkin Converts a protein sequence alignment in BLAST, CLUSTAL or MSF format for the GRASP, MOLMOL or PyMOL.

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 ClustalW2 ClustalW is a general purpose multiple sequence alignment program for DNA or proteins.

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 ClustalX Interface for ClustalW for multiple sequence alignment

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 EMBOSS Transparent retrieval of sequence data from the web

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 FASTA Protein or nucleic acid comparison

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 MOLPHY Inferring evolutionary trees from amino acid sequences

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 Muscle Multiple alignment software for protein and nucleotide sequences

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 GENEMINE GeneMine is a free sequence analysis and visualization program for web pages or presentations.

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 SCC Sequence Alignment Suite.

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 SAM Tools for creating and refining for biological sequence analysis

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 STAMP Comparison and alignment of protein three dimensional structures

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 MOLPHY Inferring evolutionary trees from sequences by Maximum Likelihood

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 Impact Enter a threshold for an alignment to indicate if a residue is "highly conserved"

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 Protein Crystallization

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 Salt Crystal Predictor Predicts salt crystals based on crystallization and commercial screen solutions Post

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 LookUp 2.0 Quickly look up crystallization contents based on condition number Post

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 MPCD Protein crystallization database Post

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 BMCD Biological macromolecule crystallization database Post

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 Gridzilla GUI-based application designed to create grid screens for protein crystal optimization

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 Data Processing

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 BEST Predicts X-ray data collection

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 BUSTER-TNT suite for crystallographic structure determination by Bayesian statistical methods

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 DPS Complete package for data processing with emphasis on synchrotrons

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 HKL2000 Data processing, space group selection, mosaicity refinement ($)

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 XIA2 Automated data reduction from raw diffraction data

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 iMOSFLM Mosflm 2.0: data reduction form X-ray images

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 LABELIT Autoindexing program designed to correct: beam center, finding a unit cell that is too large, and improperly identifying the allowed Bravais symmetry.

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 Maxit The Maxit Program Suite was developed by the PDB and NDB to assist in the processing and curation of macromolecular structure data.

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 iMOSFLM GUI for MOSFLM

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 MOSFLM Replaced by iMosflm, but is still robust for challenging cases of data processing

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 Phasing & Refinement

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 CRANK automated macromolecular structure solution

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 EPMR Finds crystallographic molecular replacement solutions using an evolutionary search algorithm

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 PHASES Computes phase angles for diffraction data from macromolecular crystals

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 SHARP Automated structure solution pipeline built around the heavy-atom refinement and phasing program SHARP, the density modification program SOLOMON, and the ARP/wARP package for automated model building and refinement (using REFMAC).

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 XPLOR-NIH A system for X-ray crystallography and NMR.

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 MOLREP Automated molecular replacement

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 REPLACE Programs for molecular replacement calculations

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 PHASER Phasing macromolecular crystal structures with maximum likelihood methods in CCP4.

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 LAFIRE Automatic refinement system for protein crystallography

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 SOMORE C-based package for solving the molecular replacement (MR) problem from X-ray crystallography.

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 BnP Automatic phasing using SnB and phases

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 SnB A dual-space direct-methods procedure for determining crystal structures

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 MAIN From initial phases to the final structure

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 CCP4 Comprehensive X-ray crystallography software suite

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 Refmac Rigid body, tls, (un)restrained refinement usually used within CCP4

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 SOLVE/RESOLVE Structure determination from scaling data to calculation of an electron density map

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 PHENIX provides tools for automated structure solution by X-ray crystallography

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 CNS X-ray crystallography: refinement, phasing, molecular replacement is the result of an international collaborative effort among several research groups

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 REPLACE A suite of programs for molecular replacement calculations.

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 HKL2MAP Graphical user-interface for macromolecular phasing with SHELX

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 SHELX Programs for crystal structure determination from single-crystal diffraction data

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 WHATIF Versatile molecular modelling package

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 XDS Processing single-crystal monochromatic diffraction data by the rotation method

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 Model Building

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 ARP/wARP Objective interpretation of crystallographic electron density maps, automatic construction and refinement of macromolecular models (usually used within CCP4).

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 Chimera interactive molecular graphics program

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 GRASP Molecular visualization and analysis particularly surface molecules and electrostatic properties

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 RAPPER Restraint-based protein modelling

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 COOT Maps and models

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 O Modeling software.

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 SCWRL3 Predicts of protein side-chain conformations.

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 XTALVIEW XtalView is a complete package for solving a macromolecular crystal structure by isomorphous replacement, including building the molecular model.

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 DSSP Defines secondary geometry (not for prediction)

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 MGLTOOLS Automated docking and molecular viewer

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 MolScript Displays 3D structures, such as proteins (schematic and detailed representations)

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 Situs Evaluate packing, within or between molecules – generates “contact dots”

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 Volslice3D 3D electron density maps. It is improved version of Volslice (part of SITUS package)

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 Probe Modelling of atomic resolution structures into low-resolution density maps

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 SPDBV Analyze several proteins at the same time

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 XDS Viewer Viewing X-ray diffraction &control images in data processing by the XDS

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 Eden Real-space electron-density refinement and optimization program

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 YASARA molecular-graphics, -modeling and -simulation program

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 Validation

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 PDB Validation The PDB Validation Suite is a set of tools used by the PDB for processing and checking structure data.

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 WHAT_CHECK Protein verification tools

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 PDBSQ Protein data bank structure validation Post

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 3DNA Building and validation of 3D nucleic acids

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 Molprobity Great program ever? Atom contacts & structure validation for proteins and DNA

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 PROCHECK Checks the stereochemical quality of a protein structure

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 PSQS Energy-like measure of the quality of protein structure

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 Figures for Pub. & Presentation

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 VMD Molecular visualization program for displaying, animating, and analyzing

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 LIGPLOT Automatic plotting protein-ligand interactions

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 PyMOL Viewing and rendering 3D structures

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 NUCCYL allows PyMOL to display models of nucleic acids in a simplified representation

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 NUCPLOT Generate schematic diagrams of protein-nucleic acid interactions

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 RNAVIEW Display the secondary structure of RNA/DNA with tertiary interactions

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 eMovie Movie plug-in tool for the molecular visualization program PyMOL Post

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 POVRAY Vision Raytracer is a high-quality, free tool for creating stunning 3D graphics

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 Rasmol Program for molecular graphics visualisation

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 Raster3D Generate high quality raster images of proteins or other molecules

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 Ribbons A popular molecular graphics software display package.

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 QTree Generates CPK, Ball and Stick and worms pictures (no shadowing)

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 Surfaces

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 HOLE Calculate pore dimensions such as in an ion channel – need PDB file

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 Surface Racer Calculates exact accessible surface area, surface area and average curvature

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 NACCESS Calculates the accessible area of a molecule from a PDB file

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 Mead Solvent effects in macromolecules by solving Poisson-Boltzmann equation

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 PISA Protein interfaces, surfaces and assemblies

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 SURFNET Generates surfaces, density contours and gap regions

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 Caver Calculates buried cavities to outside solvent in protein structures

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 MOLE Fully automated location/characterization of channels, tunnels and pores

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 Compare Structures

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 Compar CCP4 unsupported – compare two structures without having to have best fit calc.

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 Bio3D Read/write structure, sequence and dynamics trajectory data

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 LSQMAN Performs least-squares superpositioning of biomacromolecules

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 SSM A tool for protein structure comparison by pairs or multiples

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 Profit Ultimate protein least squares fitting program (rmsd fun)

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 ESCET Analyse and compare 3D structures of proteins

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 MAMMOTH-mult Aligns protein structures with 3D superimposition

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 Docking

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 3D-Dock rigid-body docking on two biomolecules to predict their correct binding geometry

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 AutoDock automated docking tools – designed to predict ligand/substrate binding

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 DOCK Explores how two molecules, such as a drug and protein receptor, might fit together

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 ZDOCK/RDOCK Protein docking

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 Protein-Nuc. Acid

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 3D-footprint Database of DNA-binding protein structures with classifications and clusters

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 BindN Prediction of DNA and RNA binding residues in proteins

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 BIPA Database for protein-nucleic acid interaction and interfaces

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 PredDNA Server for identification of DNA binding residues in protein sequences

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 DP-Bind Server for sequence-based prediction of residues in DNA-binding proteins

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 NDP Repository of three-dimensional structural information about nucleic acids

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 PDBsum Database of summaries and analyses of all PDB structures

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 ProNIT Binding data from the literature of thermodynamic data for protein-nucleic acid

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 ProNUC recognition motif of proteins and DNA forms involved in the complex (last update 06)

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 Zif-Base Database of Zinc fingers and associated references

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 Databases/Servers

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 2P2i Protein-Protein Interactions

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 Pfam Sequence annotations: input PDB ID to UniPort searches both Swiss-Prot and TrEMBL Post

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 PDBalert Web-based automatic system that alerts users as soon as a PDB structure with homology to a protein of interest becomes available Post

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 EDS Service for evaluating the electron density

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 AVP Analysis of voids in proteins and packing quality in a single united program

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 MESPEUS Coordination sites in metalloproteins that have been deposited within the PDB Post

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 Homology Servers List of the 27 most popular homology servers, according to Google PageRank Post

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 MEGAPOV Unofficial extensions to POV-RAY

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 Checkhbond Evaluates if a hydrogen bond can occur between 2 residues in a PDB structure

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 DAS Diffraction anisotropy server helps in the processing of anisotropic data Post

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 PDBTM Comprehensive and up-to-date transmembrane protein selection of the PDB

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 Bilayer Insertion Bilayer insertations of membrane proteins: PDB, organism and resolution

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 DynDom Determines domains, hinge regions in proteins when two conformations are availiable

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 SACS A Self-Maintaining Database of Antibody Crystal Structures

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 Space Group Generate space group diagrams found in the International Tables of Crystallography Post

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 TARDIS Storage of X-ray Diffraction Images Post

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 Fourier Transform Applet calculates the Fourier transform of a two dimensional density function (educational) Post

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 IMGT/3Dstructure Database related to immunoglobulins, T cell receptors, major histocompatibility complex or related proteins of the immune system Post

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 ANGULATOR Angular trends of repeat proteins

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 MCCE Protein side chain motions are simulated explicitly while the dielectric effect of solvent and bulk protein material is modeled by continuum electrostatics.

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 ValLigURL Examine if a ligand in a structure has been seen in a particular conformation Post

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 Abysis Antibody database: brings together Kabat, IMGT and structural data from the PDB Post

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 DSV Visualization of macromolecules – make figures and more Post

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 HATODAS II Heavy atom database system examines heavy atom binding motifs Post

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 ECM Enzyme catalytic mechanisms database Post

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 CSA Database that displays active sites and catalytic residues of enzymes Post

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 TLSMD TLS Refinement Post

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 REFOLD Refolding Protocols for Proteins Post

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 PDB Editor Simply and quickly edit a PDB file Post

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 metaPrDOS Predicting disordered regions in proteins Post

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 BRENDA If you study enzymes this database is must Post

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 15 Carbohydrate Databases Not atkins safe Post

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 MeRNA Metals and RNA Post

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 18 Small Molecule Databases Ligand fun Post

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 CREDO Protein-ligand interaction database for drug discovery

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 2P2I Atomic Analysis of Protein-Protein Interfaces with Known Inhibitors

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 TIMBAL Small molecules disrupting protein-protein interactions

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 Adxv Display X-ray diffraction images as 2D image, 3D wire mesh or integer pixel values

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 BABEL Interconvert molecular modeling formats, assign hybridiation, add/remove hydrogens

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 CHOOCH Calculates anomalous scattering factors for X-ray fluorescence data (SAD, MAD)

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 DELPHI Calculates protein electrostatics

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 ENTANGLE Reads PDB files then outputs interactions between nucleic-protein complexes

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 HBPLUS hydrogen bond calculations such as interactions, geometries, occupancies

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 MODULE Alignment tensor parameters for individual or multiple domains in macromolecules

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 Qnifft Macromolecular electrostatics

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 Reduce Adds hydrogens to a PDB file

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 Theseus Simultaneously superimposes multiple macromolecular structures

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 Gerard's Util Packages from RAVE, SBIN, X-UTIL, VOIDOO, DEJAVU, MAPMAN and SPASM.

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 LPC CSU Server Interatomic contacts in Ligand-Protein complexes and contacts in protein entries

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 PDBeMotif Combines protein sequence, chemical structure and 3D data in a single search

Posted by Sean | Categories: Crystallographic Data Collection, Crystallographic Data Processing, Crystallographic Data Refinement, Protein Crystallization, Scientific Publication and Presentation | Tagged: , , , |

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20 Awesome Insights so far | Have Your Say!

  1. chempilot
    April 19th, 2010 at 12:31 PM #

    awesome! thanks sean!

  2. Sean
    April 20th, 2010 at 8:59 PM #

    Thanks for the support. I have to say this post had a number of 2 am nights in it.

    I hope this list will help those searching for a particular program.

  3. j edward ladenburger
    April 20th, 2010 at 11:06 PM #

    sweet — Thanks! I’ll be sharing your hard work!

  4. Nat
    April 23rd, 2010 at 12:22 PM #

    This is an impressive list – I’ve seen similar efforts in the past but this is the most complete by far. It would be great if this could be placed on some publicly-editable Wiki or similar site so others could expand it. (License info and citations would also be useful.)

  5. Sean
    April 23rd, 2010 at 1:40 PM #

    I am more than willing to add any applicable programs to the list. Interesting idea about the wiki…

    What sort of license info would you like? Perhaps three categories: free for everyone, free/pay for academic and pay commercial

    I was trying to balance giving everyone a ton of information and having a relatively clean list to direct people to the resources. I can certainly see how highlighting certain pieces of information would save some digging (citations, pricing, manual). If anyone else has a piece of information that they would find valuable, please let me know.

    Thanks for the feedback.

  6. j edward ladenburger
    April 23rd, 2010 at 4:46 PM #

    I sent a link for this list to a wise, veteran crystallographer with a lab at Duke University and thought you would be interested in his response:

    “The young guy who does the P212121 site is just now learning crystallography. He has some neat ideas, and in as much as he just posts them, it is a sort of fun and a nice way for him to think about what he is currently learning.

    However, in as much as he posts what is indistinguishable from authoritative, well researched results, he is another example of someone junking up our mutual current and future information space.

    Besides, he didn’t mention MolProbity.. ”

    Of course, you will recognize that the negative sounding portion was largely in jest because you did not include a link to His work — He meant this as an inside joke between us — so don’t take it seriously. Note — the first comment was positive encouragement from a guy who has made significant contributions to the field.
    The main point = you might consider adding MolProbity to the list :) — You might even introduce yourself to Dave and Jane Richardson — who are very sharp and really quite delightful!!
    http://molprobity.biochem.duke.edu/

  7. Sean
    April 24th, 2010 at 3:04 PM #

    Thanks for comment. I will take ‘young’ as long as I can get it ;)

    I just finished working on my 23rd macromolecular structure unsure what qualifies as just learning. I can certainly say that I am always learning and digging for answers.

    I will reach out to them and hopefully bring back some of their insights to share. Thanks again.

  8. RFL
    April 25th, 2010 at 6:03 AM #

    Hi! thank you very much for the list!
    Some suggestions. Although they are not “xtalography related” I also find them very useful when working on new constructs and so on:

    Transform: a very simple and easy to use program for the manipulation of sequences (http://www.ahatfullofsky.comuv.com/English/Programs/Transform/Transform.html)
    EnzymeX and 4Peaks (http://mekentosj.com/science/enzymex/)
    Amplify (simulate PCR) (http://engels.genetics.wisc.edu/amplify/)

  9. DrSNO
    April 25th, 2010 at 4:16 PM #

    “I just finished working on my 23rd macromolecular structure”
    Are you working on lysozyme?
    Rob Sweet (NSLS) used to say, “you only have 10 structure in your body (grad +post-doc), choose them wisely. Now this goes completely against what Brian Matthews was up to with lysozyme. But he wasn’t the one solving the structures…

  10. Sean
    April 25th, 2010 at 4:43 PM #

    I didn’t count lysozyme :)

  11. Sean
    April 28th, 2010 at 5:14 PM #

    Hi RFL,

    Thanks for the suggestions! I have added the programs you mentioned.

  12. Sean
    May 2nd, 2010 at 3:55 PM #

    Just added 11 more programs.

  13. Sean
    May 18th, 2010 at 10:19 PM #

    Added 15 more entries and crossed the 250 mark!

  14. Vijay
    May 17th, 2011 at 11:48 AM #

    Valuable additions to this list can be protein crystallization prediction servers like – XtalPred, CRYSTALP2, SSPF Crystallisation Propensity Predictor, SECRET and so on.

  15. Sean
    May 17th, 2011 at 2:13 PM #

    Hi Vijay,

    Good idea! Have you found them useful? Care to elaborate on the ‘and so on’?

    Thanks for suggestions.

  16. sr
    October 7th, 2011 at 12:04 AM #

    I found this program very useful……

    ALIGN: a program to superimpose protein coordinates, accounting for insertions and deletions
    G. H. Cohen

  17. Sean
    October 7th, 2011 at 12:06 AM #

    Hi sr,

    Thanks buddy! I will have to give it a look and put it up!

  18. Ethan Merritt
    October 12th, 2011 at 2:06 PM #

    Sequence Tools:
    TeXshade
    TeX-based generation of sequence alignments for publication.
    Validation:
    Parvati Validation server for B factors from anisotropic refinement or TLS
    Protein Crystallization:
    Prospero Prediction of crystallization success based on biophysical characterization of the sample

  19. Ethan Merritt
    October 12th, 2011 at 2:32 PM #

    Hmm. That first link got mangled. Let’s try again:
    TeXshadeTeX-based annotation of multiple sequence alignments for publication.
    Compare Structures:
    <a href="http://www.ncbi.nlm.nih.gov/Structure/VAST/"VASTstructure superposition and similarity recognition

  20. Pavel
    December 1st, 2011 at 1:34 AM #

    Hi,

    what about MOLLY, MOPRO, XD, FROG, TEXTAL… ?

    In your classification: PHENIX is in “Phasing & Refinement” but not in “Model building” and “Validation”. FYI: Molprobity is part of PHENIX.

    “Figures for publication..”: I know people that still use SETOR for doing pretty pictures, and use CHAIN for model building (I used to use it too).

    Pavel

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