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3D-Dock Suite
FTDock, RPScore and MultiDock
3DNA calculates a complete set of local base-pair, step, and helical parameters, and allows for exact rebuilding of a structure based on these parameters.
DNA is a versatile package for the analysis, rebuilding, and visualization of three-dimensional nucleic acid structures, based on a standard reference frame.
A la mode
A La Mode is an environment for building models of ligand and monomer molecular components. Databases for monomer units and ligands are under construction. A searchable database for the nucleotide units is available.
ab initio procedure for the determination of protein structure using atomic resolution data, and for finding sub-structures from anomalous or isomorphous differences.
ACT is a program that analyzes coordinates. It provides B-factor statistics and finds all crystal contacts.
The web application AISMIG (An Interactive Server-side Molecule Image Generator) is a new way of molecule image generation.
ALINE is a protein-sequence alignment editor for publication-quality alignments.
AMoRe (Automatic Molecular Replacement) is a software package to solve protein structures via molecular replacement.
ARP/wARP is a software suite for improvement and objective interpretation of crystallographic electron density maps and automatic construction and refinement of macromolecular models.
Amber is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules.
AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
BUSTER is a software system for crystallographic structure determination by Bayesian statistical methods.
Bioinformatics tools
Bioinformatics tools from the Israel Structural Proteomics Center.
Biological Macromolecule Crystallization Database Version 4 (BMCD4)
The Biological Macromolecule Crystallization Database Version 4 (BMCD4) compiles crystallization conditions from the literature.
Biological Magnetic Resonance Data Bank (BMRB)
A Repository for Data from NMR Spectroscopy on Proteins, Peptides, and Nucleic Acids.
Biomolecular Object Network Databank (BOND)
Biomolecular Object Network Databank (BOND) is a resource that integrates sequence and interaction information.
Robert Esnouf's extensions to MolScript (v 1.4) including color ramping.
CATH is a novel hierarchical classification of protein domains.
The CCP4 (Collaborative Computational Project Number 4 in Protein Crystallography) program suite is a collection of programs covering most of the computations required for macromolecular crystallography.
CLIMS (Laboratory Information Management System) for protein Crystallography that features a novel graphical interface to a relational database, and assists all aspects of protein crystallisation, including: 1) protein expression and handling; 2) crystallisation optimisation; and 3) visualisation of results and preliminary diffraction data.
Crystallography & NMR System (CNS) provides convient access to the most commonly used algorithms in macromolecular structure determination.
The Crystallography Open Database (COD) curently has 48,000 entries.
COMO is a program for molecular replacement calculations, which uses the combined molecular replacement protocol.
CRANK is a suite of programs for automated macromolecular structure solution. Crank is also designed to help teach novice users about the various programs used in crystallography.
Cameron Mura's PyMOL Scripts
PyMOL examples are illustrated here in the form of input macros (.pml files) and their corresponding graphical outputs (.png files).
ChemDB is a public database of small molecules available on the Web. In 2005 the database contained approximately 4.1 million commercially available compounds.
Chimera is an interactive molecular graphics program, which is the successor to UCSF Midas and MidasPlus.
First fully automated Protein-Protein Docking web server.
Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service.
ConSurf Server
Identification of functional regions in proteins by surface-mapping of phylogenetic information.
Coot (Crystallographic Object-Oriented Toolkit) is for model building, model completion, and validation.
Cryoprotectant database for protein crystals
This web site is a compilation of cryoprotection conditions.
Crystal Growth 101 literature from Hampton Research
Are you looking to get started in crystallization? Check out some of Hampton Reseearch's Crystal Growth 101 guides to help you.
Crystallization Tips
A collection of crystallization tips from Hampton Research.
Curves calculates a helical parameter description for any nucleic acid segment with respect to an optimal, global helical axis.
DINO is a realtime 3D visualization program for structural biology data.
The Dowser program surveys a protein molecule's structure to locate internal cavities and assess the hydrophilicity of these cavities in terms of the energy of interaction of a water molecule with the surrounding atoms.
The DSSP program automates protein secondary structure assignment from PDB structures.
The Dali server compares protein structures in 3D.
Detwin tests for merohedral twinning and detwins data.
DisEMBL is a computational tool for prediction of disordered/unstructured regions within a protein sequence. As no clear definition of disorder exists, we have developed parameters based on several alternative definitions, and introduced a new one based on the concept of ``hot loops'', i.e. coils with high temperature factors.
DisProt is a database of proteins that lack fixed 3D structure in their native state.
Disulphide Database (DSDBASE)
DSDBASE is a database on disulphide bonds in proteins.
DM is a density modification program.
The DrugBank database combines drug data with drug target information.
EGAD: protein design and mutant stability and affinity prediction
EGAD is a free, open-source software package for protein design and prediction of mutation effects on protein folding stabilities and binding affinities to 1kcal/mol. EGAD can also consider multiple structures simultaneously for designing specific binding proteins or locking proteins into specific conformational states. In addition to natural protein residues, EGAD can also consider free-moving ligands with or without rotatable bonds.
EPMR (Evolutionary Programming for Molecular Replacement)
"EPMR is a program that finds crystallographic molecular replacement solutions using an evolutionary search algorithm. The program directly optimizes the three rotational and three positional parameters for the search model with respect to the correlation coefficient between Fo and Fc."
ERRAT Structure Verification Server
ERRAT is a protein structure verification algorithm that works by analyzing the statistics of non-bonded interactions between different atom types.
ESPript (Easy Sequencing in Postscript) is a utility to generate a pretty PostScript output from aligned sequences.
Eden (short for Electron density) is uses a real-space method in the search for a crystal structure.
Electron Density Server
The Uppsala Electron Density Server can be used to readily obtain electron density maps of deposited structures.
WebFEATURE allows a user to scan a molecular structure for a particular functional site.
FoldIndex tries to answer to the question: Will this protein fold? It's a dynamic and interactive process that estimates the local and general probability for the provided sequence, under specified conditions, to fold.
GDAP (Genomic Disulfide Analysis Program) provides web access to computationally predicted protein disulfide bonds for over one hundred microbial genomes, including both bacterial and achaeal species.
Intrinsic Protein Disorder, Domain & Globularity Prediction.
GRASP is a molecular visualization and analysis program. It is particularly useful for the display and manipulation of the surfaces of molecules and their electrostatic properties.
Gareth Stockwell's PyMOL Scripts
This page contains some resources for the PyMOL molecular graphics program.
The Heavy Atom Databank (HAD) is a compilation of conditions used for the preparation of heavy atom derivatives.
HATODAS (Heavy Atom Database System) was designed to help the process of finding useful heavy atom derivatives.
HBexplore is a tool to identify and then analyze hydrogen bonds in biological macromolecules.
Integrated suite for the merging and scaling of diffracted intensities.
HKL-2000 is a new program package based on the extended versions of Denzo, Xdisplayf and Scalepack.
HWI High Throughput Crystallization Service
The high-throughput crystallization laboratory at HWI will prepare crystal-growth screening experiments in 1536-well microassay plates free to anyone who will permit the results of the experiment to be added to the HWI crystallization database. This service is otherwise provided for a fee of $1,000 per plate. We will not publicly disclose information on any sample we receive for crystallization trials without the expressed written consent of the investigator(s).
Heavy Atom Reagents Database
Heavy Atom Reagents Database comprises 87 reagents and 30 different heavy atoms.
Hetero-compound Information Centre - Uppsala (HIC-Up)
HIC-Up provides coordinate and dictionary files for most small molecules.
HySS (Hybrid Substructure Search) is a module of the Phenix package. It is used for the location of anomalous scatterers in macromolecular structures.
The Inorganic Crystal Structure Database (ICSD) comprises more than 90,000 inorganic structures.
Insight II
Insight II provides a comprehensive, integrated molecular graphics environment for visualization, protein engineering, macromolecular simulations, homology modeling, and de novo ligand design, enabling researchers to gain early insights into the structure and function of their targets of interest.
Jmol is a free, cross-platform, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry.
A "kinemage" (kinetic image) is a scientific illustration presented as an interactive computer display.
KiNG (Kinemage, Next Generation) is an interactive system for three-dimensional vector graphics.
Kristian Rother's PyMOL Plugins
PyMOL plugins.
LIGPLOT automatically generates diagrams of protein-ligand interactions from a PDB file.
Ligand Depot
Ligand Depot is a data warehouse which integrates databases, services, tools and methods related to small molecules bound to macromolecules.
MAID builds the protein structure into the electron-density map in a series of sequential steps.
MAIN is a very powerful program and a programming language which provides tools in the form of macros to diagnose many of your crystallographical problems.
MERNA is a database of metal ion binding in RNA.
MIFit was originally developed by Duncan McRee as a replacement for his popular xfit program.
MLPHARE (maximum likelihood heavy atom refinement and phase calculation) refines heavy atom parameters and error estimates.
MOLREP performs molecular replacement in two steps: Rotation function followed by cross translation and packing functions.
MOSFLM is used for processing image plate and CCD data. It determines the crystal orientation, cell parameters, and space group. It also generates a list of reflections.
MPCD (Marseille Protein Crystallization Database) combines two crystallization databases, CYCLOP and BMCD (v2.0).
MSD Ligand Chemistry
MSD Ligand Chemistry is a library of ligands, small molecules and monomers that are referred as residues and hetgroups in any PDB entry.
This jiffy calculates probabilities for the occurrence of multimers in a crystal asymmetric unit.
Metalloprotein Database and Browser (MDB)
MDB contains quantitative information on all the metal-containing sites available from structures in the PDB distribution.
Michael Lerner's PyMOL Scripts
Some useful PyMOL scripts.
Using a sequence alignment, MODELLER generates a homology model.
Web service for all-atom contact and geometrical analysis of your model.
MolScript is a program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations.
NCI open database
NCI open database is a WWW browser to the new and enlarged collection of open NCI database compounds (>250,000 structures).
NDB (Nucleic acid DataBase) is a repository of three-dimesional structural information about nucleic acids.
The menu-driven operation of NOC makes it easy to use and flexible environment to explore macromolecular structures.
NUCPLOT generate schematic diagrams of protein-nucleic acid interactions from a given PDB file.
O is a macromolecular crystallographic modeling tool by Alwyn Jones.
PARVATI (Protein Anisotropic Refinement Validation and Analysis Tool) is a validation/analysis tool for macromolecular structure refinements that include anisotropic displacement parameters.
PDB Editor
PDB Editor can be used to search, select, extract and edit information from PDB files.
PISA (Protein Interfaces, Surfaces and Assemblies) is an interactive tool for the exploration of macromolecular (protein, DNA/RNA and ligand) interfaces, prediction of probable quaternary structures (assemblies), database searches of structurally similar interfaces and assemblies, as well as searches on various assembly and PDB entry parameters.
Disordered regions (DRs) are entire proteins or regions of proteins which lack a fixed tertiary structure, essentially being partially or fully unfolded.
POODLE (Prediction Of Order and Disorder by machine LEarning) is a system that predicts disorder regions using amino acid sequence alone. The POODLE system consists of three predictions, short disorder regions prediction, long disorder regions prediction and unfolded protein prediction.
Protein fold similarity Web server
The PRODRG server will convert coordinates for small molecules in PDB format to the following topology formats: GROMOS, GROMACS, WHAT IF, REFMAC5, CNS, O, SHELX, HEX and MOL2. In addition, coordinates for hydrogen atoms are generated.
Pdbfun is a web server for the identification of local structural similarities among annotated residues in proteins.
"Phaser is a program for phasing macromolecular crystal structures with maximum likelihood methods. It currently has methods for brute force and fast likelihood-based rotation and translation functions for molecular replacement."
PiQSi is a community effort that facilitates the investigation and curation of quaternary structures.
Protein Data Bank (PDB)
Repository for the processing and distribution of 3-D structural data from biological macromolecules.
Protein Loop Classification
This database of 200+ proteins classifies loops into five types according to their secondary structure.
Protein Movie Generator
Protein Movie Generator (PMG) is a service that can generate pictures and movies of protein structures.
PyMOL is a molecular viewer with the ability to generate high-quality rendered images for publication or animations, as well as other common molecular graphics activities to support crystallography.
Queen of Spades
The program `Queen of Spades' , is an attempt to write a multi-dimensional, multi-model, space-group general, molecular (re)placement program.
RANTAN is a direct method program for the determination of heavy atom positions in a macro-molecular structure. It can also be used to determine small molecule structures.
REFMAC is a macromolecular refinement program, which can carry out rigid body, TLS, restrained or unrestrained refinement against X-ray data.
The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.
Regional Order Neural Network (RONN) to predict protein disorder.
RaCC (Rare Codon Calculator) determines the number of rare E. coli codon in a given DNA sequence.
RasMol & OpenRasMol
RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules.
RasTop is a molecular visualization software derived from Rasmol.
Raster3D is a set of tools for generating high quality raster images of proteins or other molecules.
Reciprocal Net
The Reciprocal Net is a distributed database used by research crystallographers to store information about molecular structures; much of the data is available to the general public.
Refold is a database of refolding protocols for a wide variety of proteins.
REPLACE is a suite of programs for molecular replacement calculations.
The Ribbons software interactively displays molecular models, analyzes crystallographic results, and creates publication quality images.
Robert L. Campbell's PyMOL Scripts
Included below are some PyMOL tools to create the drawing commands to show the symmetry axes for a crystal, to draw a fancier unit cell and an attempt at drawing reciprocal space in 3D.
SCALA scales together multiple observations of reflections, and merges multiple observations into an average intensity.
SETOR is designed to allow the display of secondary, tertiary and quaternary structures of protein and nucleic acid macromolecules, and to allow a wide variety of rendering models to be used.
autoSHARP is an automated structure solution pipeline. SHARP refines heavy atom sites and calculates phases.
The SHELX suite of programs for macromolecular structure determination includes modules for the determination of substructure structure factors (SHELXC), substructure solution (SHELXD), phase calculation, and density modification (SHELXE).
SOLVE: Automated crystallographic structure solution for MIR, SAD, and MAD; RESOLVE: Statistical density modification, local pattern matching, automated model-building, automated ligand-fitting, and prime-and-switch minimum bias phasing
SOMoRe (Search and Optimization Molecular Replacement) uses a six-dimensional approach to solve a molecular replacement problem.
STING Millennium
STING Millennium is a web based suite of programs that starts with visualizing molecular structure and then leads a user through a series of operations resulting in a comprehensive structure analysis.
Sweet is a program for constructing 3D models of saccharides from their sequences using standard nomenclature.
SYBYL is a suite of computational informatics software designed to enhance the drug discovery workflows and decision-making of today's computational chemists and molecular modelers.
SnB is a computer program based on Shake-and-Bake, a dual-space direct-methods procedure for determining crystal structures from X-ray diffraction data.
Structural Classification of Proteins (SCOP)
The SCOP aims to provide a description of the structural and evolutionary relationships between all protein structures.
SWISS-MODEL is a fully automated protein structure homology-modeling server, accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer).
Symmetry Equivalent Molecules
A web based GUI to generate and visualize the macromolecules.
TLS Motion Determination
TLS Motion Determination (TLSMD) analyzes a protein crystal structure for evidence of flexibility, e.g. local or inter-domain motions.
TNT is a general purpose refinement package used in the solution of macromolecular structures using X-ray crystallography.
TRUNCATE is used to generate structure factor amplitudes from a list of intensities. The Wilson plot part of the program attempts to calculate an absolute scale and temperature factor from a set of observed intensities.
TargetDB is a protein target registration database. It provides status and tracking information on the progress of the production and solutions of protein structures.
The Buffalo 'n Pittsbugh Interface for protein phasing (BnP)
The BnP interface couples SnB to appropriate components of the PHASES suite, thereby creating an automated pipeline from intensity data to an unambiguous protein electron-density map.
The Merohedral Crystal Twinning Server
The Protein Crystallization Home Page of Terese Bergfors
The Protein Crystallization Page includes a pictorial library of crystallization drop phenomena.
Topology Cartoon Server
This service allows you to submit a protein structure for calculation of the topology cartoon.
Turbo-Frodo is a general-purpose molecular modeling environment.
Uppsala Software Factory (Gerard Kleywegt)
Gerard Kleywegt's site (USF) with programs and other links handy for macromolecular crystallography.
VaZyMolO is a database dealing with viral sequences at the protein level. Its aim is to define modules suitable for high expression, solubility, and crystallization.
This web site describes various icosahedral virus capsid structures in the Protein Data Bank (PDB) in terms of their complete capsids, detailed structural and computational analysis
VMD (Visual Molecular Dynamics) is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
Verify3D Structure Evaluation Server
Verify3D (UCLA-DOE) server is a tool designed to help in the refinement of crystallographic structures.
WHAT IF is a versatile molecular modeling package that is specialized on working with proteins and the molecules in their environment like water, ligands, nucleic acids, etc.
WHAT_CHECK is a downloadable structure valiadation suite based upon the DSSP and WHAT IF programs.
X-PLOR's main focus is the three-dimensional structure determination of macromolecules using crystallographic diffraction or nuclear magnetic resonance (NMR) data.
X-ray Detector Software (XDS) processes single-crystal monochromatic diffraction data recorded by the rotation method.
XPREP is used to evaluate diffraction data. It can also detect twinning.
XtalView is a complete package for solving a macromolecular crystal structures (not currently supported).
ZDOCK includes two protein docking algorithms, designed to operate in succession: a rigid-body docking program and a refinement program.
ZINC is a free database of commercially-available compounds for virtual screening. ZINC contains over 4.6 million compounds in ready-to-dock, 3D formats.
d*TREK is a flexible, customizable, device-independent software suite and toolkit which processes single crystal X-ray diffraction images from two-dimensional position sensitive detectors.
The eHiTS (electronic High Throughput Screening) software provides flexible ligand docking at speed approaching the crude virtual high throughput screening methods.
eMovie is a tool for making molecular movies with PyMOL.
vmd-xplor NMR Visualization
The vmd-xplor package is a combination of the X-PLOR structure determination program and VMD (Visual Molecular Dynamics).