Subscriptions

Last updated:
April 11, 2024 07:12 AM
All times are UTC.



Powered by:
Planet

UVM Home Page
© Copyright 2009

Structural > Phasing

ACORN
ab initio procedure for the determination of protein structure using atomic resolution data, and for finding sub-structures from anomalous or isomorphous differences.
AMoRe
AMoRe (Automatic Molecular Replacement) is a software package to solve protein structures via molecular replacement.
ARP/wARP
ARP/wARP is a software suite for improvement and objective interpretation of crystallographic electron density maps and automatic construction and refinement of macromolecular models.
CNS
Crystallography & NMR System (CNS) provides convient access to the most commonly used algorithms in macromolecular structure determination.
COMO
COMO is a program for molecular replacement calculations, which uses the combined molecular replacement protocol.
CRANK
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.
Dm
DM is a density modification program.
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."
Eden
Eden (short for Electron density) is uses a real-space method in the search for a crystal structure.
HySS
HySS (Hybrid Substructure Search) is a module of the Phenix package. It is used for the location of anomalous scatterers in macromolecular structures.
MAID
MAID builds the protein structure into the electron-density map in a series of sequential steps.
MLPHARE
MLPHARE (maximum likelihood heavy atom refinement and phase calculation) refines heavy atom parameters and error estimates.
MOLREP
MOLREP performs molecular replacement in two steps: Rotation function followed by cross translation and packing functions.
Phaser
"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."
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
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.
Replace
REPLACE is a suite of programs for molecular replacement calculations.
SHARP/AutoSHARP
autoSHARP is an automated structure solution pipeline. SHARP refines heavy atom sites and calculates phases.
SHELX
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/RESOLVE
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
SOMoRe (Search and Optimization Molecular Replacement) uses a six-dimensional approach to solve a molecular replacement problem.
SnB
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.
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.
X-PLOR
X-PLOR's main focus is the three-dimensional structure determination of macromolecules using crystallographic diffraction or nuclear magnetic resonance (NMR) data.
XPREP
XPREP is used to evaluate diffraction data. It can also detect twinning.
vmd-xplor NMR Visualization
The vmd-xplor package is a combination of the X-PLOR structure determination program and VMD (Visual Molecular Dynamics).