Ultimate List of Crystallography Related Programs

18 April 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

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