Protein Data Bank (PDB): the single global macromolecular structure archive
Abstract The Protein Data Bank (PDB)––the single global repository of experimentally
determined 3D structures of biological macromolecules and their complexes––was …
determined 3D structures of biological macromolecules and their complexes––was …
ACPYPE-Antechamber python parser interface
AW Sousa da Silva, WF Vranken - BMC research notes, 2012 - Springer
Abstract Background ACPYPE (or AnteChamber PYthon Parser interfacE) is a wrapper
script around the ANTECHAMBER software that simplifies the generation of small molecule …
script around the ANTECHAMBER software that simplifies the generation of small molecule …
Cyclization of conotoxins to improve their biopharmaceutical properties
Conotoxins are disulfide-rich peptides from the venoms of marine cone snails that are used
in prey capture. Due to their exquisite potency and selectivity for different ion channels …
in prey capture. Due to their exquisite potency and selectivity for different ion channels …
Generalized fragment picking in Rosetta: design, protocols and applications
The Rosetta de novo structure prediction and loop modeling protocols begin with coarse
grained Monte Carlo searches in which the moves are based on short fragments extracted …
grained Monte Carlo searches in which the moves are based on short fragments extracted …
PDBe: protein data bank in Europe
S Velankar, C Best, B Beuth… - Nucleic acids …, 2010 - academic.oup.com
ABSTRACT The Protein Data Bank in Europe (PDBe)(http://www. ebi. ac. uk/pdbe/) is
actively working with its Worldwide Protein Data Bank partners to enhance the quality and …
actively working with its Worldwide Protein Data Bank partners to enhance the quality and …
CING: an integrated residue-based structure validation program suite
JF Doreleijers, AW Sousa da Silva, E Krieger… - Journal of biomolecular …, 2012 - Springer
We present a suite of programs, named CING for Common Interface for NMR Structure
Generation that provides for a residue-based, integrated validation of the structural NMR …
Generation that provides for a residue-based, integrated validation of the structural NMR …
ARIA for solution and solid-state NMR
In solution or solid-state, determining the three-dimensional structure of biomolecules by
Nuclear Magnetic Resonance (NMR) normally requires the collection of distance …
Nuclear Magnetic Resonance (NMR) normally requires the collection of distance …
NMR Exchange Format: a unified and open standard for representation of NMR restraint data
A Gutmanas, PD Adams, B Bardiaux… - Nature structural & …, 2015 - nature.com
In addition to the restraints data, NEF requires polymer sequence information and
chemicalshift assignments, and allows inclusion of peak lists. A compliant NEF file contains …
chemicalshift assignments, and allows inclusion of peak lists. A compliant NEF file contains …
Improved reliability, accuracy and quality in automated NMR structure calculation with ARIA
In biological NMR, assignment of NOE cross-peaks and calculation of atomic conformations
are critical steps in the determination of reliable high-resolution structures. ARIA is an …
are critical steps in the determination of reliable high-resolution structures. ARIA is an …
Archiving and disseminating integrative structure models
Limitations in the applicability, accuracy, and precision of individual structure
characterization methods can sometimes be overcome via an integrative modeling …
characterization methods can sometimes be overcome via an integrative modeling …