Automatic rebuilding and optimization of crystallographic struc- tures in the PDB
نویسندگان
چکیده
Motivation: Macromolecular crystal structures in the Protein Data Bank (PDB) are a key source of structural insight into biological processes. These structures, some more than 30 years old, were constructed with methods of their era. With PDB_REDO we aim to automatically optimize these structures to better fit their corresponding experimental data, passing the benefits of new methods in crystallography on to a wide base of non-crystallographer structure us-
منابع مشابه
Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank
MOTIVATION Macromolecular crystal structures in the Protein Data Bank (PDB) are a key source of structural insight into biological processes. These structures, some >30 years old, were constructed with methods of their era. With PDB_REDO, we aim to automatically optimize these structures to better fit their corresponding experimental data, passing the benefits of new methods in crystallography ...
متن کاملProduct of derivations on C$^*$-algebras
Let $mathfrak{A}$ be an algebra. A linear mapping $delta:mathfrak{A}tomathfrak{A}$ is called a textit{derivation} if $delta(ab)=delta(a)b+adelta(b)$ for each $a,binmathfrak{A}$. Given two derivations $delta$ and $delta'$ on a $C^*$-algebra $mathfrak A$, we prove that there exists a derivation $Delta$ on $mathfrak A$ such that $deltadelta'=Delta^2$ if and only if either $delta'=0$ or $delta=sdel...
متن کاملPDB_REDO: constructive validation, more than just looking for errors
Developments of the PDB_REDO procedure that combine re-refinement and rebuilding within a unique decision-making framework to improve structures in the PDB are presented. PDB_REDO uses a variety of existing and custom-built software modules to choose an optimal refinement protocol (e.g. anisotropic, isotropic or overall B-factor refinement, TLS model) and to optimize the geometry versus data-re...
متن کاملThe PDB_REDO server for macromolecular structure model optimization
The refinement and validation of a crystallographic structure model is the last step before the coordinates and the associated data are submitted to the Protein Data Bank (PDB). The success of the refinement procedure is typically assessed by validating the models against geometrical criteria and the diffraction data, and is an important step in ensuring the quality of the PDB public archive [R...
متن کاملTools for interactive map conversion and vectorization
The process of converting an analog map into struc tured digitized information requires several di erent operations which are all time consuming when per formed manually Strictly automatic processing is not always a possible solution and an interactive approach can then be an alternative This paper describes a tool for map conversion fo cusing on the functionality for extraction of line struc t...
متن کامل