Cargando…

Modelling covalent linkages in CCP4

In this contribution, the current protocols for modelling covalent linkages within the CCP4 suite are considered. The mechanism used for modelling covalent linkages is reviewed: the use of dictionaries for describing changes to stereochemistry as a result of the covalent linkage and the application...

Descripción completa

Detalles Bibliográficos
Autores principales:	Nicholls, Robert A., Joosten, Robbie P., Long, Fei, Wojdyr, Marcin, Lebedev, Andrey, Krissinel, Eugene, Catapano, Lucrezia, Fischer, Marcus, Emsley, Paul, Murshudov, Garib N.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	International Union of Crystallography 2021
Materias:	Ccp4
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8171069/ https://www.ncbi.nlm.nih.gov/pubmed/34076587 http://dx.doi.org/10.1107/S2059798321001753

Ejemplares similares

The missing link: covalent linkages in structural models
por: Nicholls, Robert A., et al.
Publicado: (2021)

GEMMI and Servalcat restrain REFMAC5
por: Yamashita, Keitaro, et al.
Publicado: (2023)

Predicted models and CCP4
por: Simpkin, Adam J., et al.
Publicado: (2023)

CCP4 Cloud for structure determination and project management in macromolecular crystallography
por: Krissinel, Eugene, et al.
Publicado: (2022)

The CCP4 suite: integrative software for macromolecular crystallography
por: Agirre, Jon, et al.
Publicado: (2023)

Local and global analysis of macromolecular atomic displacement parameters
por: Masmaliyeva, Rafiga C., et al.
Publicado: (2020)

Cryo-EM single-particle structure refinement and map calculation using Servalcat
por: Yamashita, Keitaro, et al.
Publicado: (2021)

Atomic model validation using the CCP-EM software suite
por: Joseph, Agnel Praveen, et al.
Publicado: (2022)

Using Phaser and ensembles to improve the performance of SIMBAD
por: Simpkin, Adam J., et al.
Publicado: (2020)

Model building and beyond
por: Agirre, Jon, et al.
Publicado: (2022)

Analysis and validation of overall N-glycan conformation in Privateer
por: Dialpuri, Jordan S., et al.
Publicado: (2023)

LAHMA: structure analysis through local annotation of homology-matched amino acids
por: van Beusekom, Bart, et al.
Publicado: (2021)

New restraints and validation approaches for nucleic acid structures in PDB-REDO
por: de Vries, Ida, et al.
Publicado: (2021)

Development and assessment of CootVR, a virtual reality computer program for model building
por: Todd, Hamish, et al.
Publicado: (2021)

FLEXR: automated multi-conformer model building using electron-density map sampling
por: Stachowski, Timothy R., et al.
Publicado: (2023)

Structural barriers to scientific progress
por: Cowtan, K.
Publicado: (2020)

Density modification of cryo-EM maps
por: Terwilliger, Thomas C., et al.
Publicado: (2020)

Fragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER
por: Richards, Logan S., et al.
Publicado: (2020)

Predicting protein model correctness in Coot using machine learning
por: Bond, Paul S., et al.
Publicado: (2020)

Structural alphabets for conformational analysis of nucleic acids available at dnatco.datmos.org
por: Černý, Jiří, et al.
Publicado: (2020)

Pairwise running of automated crystallographic model-building pipelines
por: Alharbi, Emad, et al.
Publicado: (2020)

Molecular replacement using structure predictions from databases
por: Simpkin, Adam J., et al.
Publicado: (2019)

Non-merohedral twinning: from minerals to proteins
por: Sevvana, Madhumati, et al.
Publicado: (2019)

SEQUENCE SLIDER: expanding polyalanine fragments for phasing with multiple side-chain hypotheses
por: Borges, Rafael Junqueira, et al.
Publicado: (2020)

ALIXE: a phase-combination tool for fragment-based molecular replacement
por: Millán, Claudia, et al.
Publicado: (2020)

Estimating local protein model quality: prospects for molecular replacement
por: Wallner, Björn
Publicado: (2020)

A practical overview of molecular replacement: Clostridioides difficile PilA1, a difficult case study
por: Crawshaw, Adam D., et al.
Publicado: (2020)

The use of local structural similarity of distant homologues for crystallographic model building from a molecular-replacement solution
por: Chojnowski, Grzegorz, et al.
Publicado: (2020)

Measuring and using information gained by observing diffraction data
por: Read, Randy J., et al.
Publicado: (2020)

ALEPH: a network-oriented approach for the generation of fragment-based libraries and for structure interpretation
por: Medina, Ana, et al.
Publicado: (2020)

Extending the scope of coiled-coil crystal structure solution by AMPLE through improved ab initio modelling
por: Thomas, Jens M. H., et al.
Publicado: (2020)

How far are we from automatic crystal structure solution via molecular-replacement techniques?
por: Burla, Maria Cristina, et al.
Publicado: (2020)

Factors influencing estimates of coordinate error for molecular replacement
por: Hatti, Kaushik S., et al.
Publicado: (2020)

Integrated, rational molecular replacement
por: Usón, Isabel, et al.
Publicado: (2021)

Detection of translational noncrystallographic symmetry in Patterson functions
por: Caballero, Iracema, et al.
Publicado: (2021)

Phasertng: directed acyclic graphs for crystallographic phasing
por: McCoy, Airlie J., et al.
Publicado: (2021)

Using a partial atomic model from medium-resolution cryo-EM to solve a large crystal structure
por: Fàbrega-Ferrer, Montserrat, et al.
Publicado: (2021)

TEMPy2: a Python library with improved 3D electron microscopy density-fitting and validation workflows
por: Cragnolini, Tristan, et al.
Publicado: (2021)

CERES: a cryo-EM re-refinement system for continuous improvement of deposited models
por: Liebschner, Dorothee, et al.
Publicado: (2021)

High-performance macromolecular data delivery and visualization for the web
por: Sehnal, David, et al.
Publicado: (2020)

Cannot write session to /tmp/vufind_sessions/sess_c33s4j55jcnfqv6gulp26amjhc