Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination
A Wlodawer, W Minor, Z Dauter… - The FEBS journal, 2013 - Wiley Online Library
The number of macromolecular structures deposited in the Protein Data Bank now
approaches 100 000, with the vast majority of them determined by crystallographic methods …
approaches 100 000, with the vast majority of them determined by crystallographic methods …
A brief history of macromolecular crystallography, illustrated by a family tree and its N obel fruits
M Jaskolski, Z Dauter, A Wlodawer - The FEBS journal, 2014 - Wiley Online Library
As a contribution to the celebration of the year 2014, declared by the United Nations to be
'The International Year of Crystallography', the FEBS Journal is dedicating this issue to …
'The International Year of Crystallography', the FEBS Journal is dedicating this issue to …
Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA, and Z-DNA
M Krepl, M Zgarbová, P Stadlbauer… - Journal of chemical …, 2012 - ACS Publications
Refinement of empirical force fields for nucleic acids requires their extensive testing using as
wide range of systems as possible. However, finding unambiguous reference data is not …
wide range of systems as possible. However, finding unambiguous reference data is not …
Mg2+ ions: do they bind to nucleobase nitrogens?
Given the many roles proposed for Mg2+ in nucleic acids, it is essential to accurately
determine their binding modes. Here, we surveyed the PDB to classify Mg2+ inner-sphere …
determine their binding modes. Here, we surveyed the PDB to classify Mg2+ inner-sphere …
Polarizable force field for DNA based on the classical Drude oscillator: II. Microsecond molecular dynamics simulations of duplex DNA
JA Lemkul, AD MacKerell Jr - Journal of chemical theory and …, 2017 - ACS Publications
The structure and dynamics of DNA are governed by a sensitive balance between base
stacking and pairing, hydration, and interactions with ions. Force-field models that include …
stacking and pairing, hydration, and interactions with ions. Force-field models that include …
Stereochemistry and validation of macromolecular structures
A Wlodawer - Protein Crystallography: Methods and Protocols, 2017 - Springer
Macromolecular structure is governed by the strict rules of stereochemistry. Several
approaches to the validation of the correctness of the interpretation of crystallographic and …
approaches to the validation of the correctness of the interpretation of crystallographic and …
Lone pair… π contacts and structure signatures of r (UNCG) tetraloops, Z-turns, and Z-steps: a WebFR3D survey
CL Zirbel, P Auffinger - Molecules, 2022 - mdpi.com
Z-DNA and Z-RNA have long appeared as oddities to nucleic acid scientists. However, their
Z-step constituents are recurrently observed in all types of nucleic acid systems including …
Z-step constituents are recurrently observed in all types of nucleic acid systems including …
Cryo neutron crystallography demonstrates influence of RNA 2′-OH orientation on conformation, sugar pucker and water structure
The ribose 2′-hydroxyl is the key chemical difference between RNA and DNA and primary
source of their divergent structural and functional characteristics. Macromolecular X-ray …
source of their divergent structural and functional characteristics. Macromolecular X-ray …
ACHESYM: an algorithm and server for standardized placement of macromolecular models in the unit cell
M Kowiel, M Jaskolski, Z Dauter - Acta Crystallographica Section D …, 2014 - journals.iucr.org
Despite the existence of numerous useful conventions in structural crystallography, for
example for the choice of the asymmetric part of the unit cell or of reciprocal space …
example for the choice of the asymmetric part of the unit cell or of reciprocal space …
[PDF][PDF] Avoidable errors in deposited macromolecular structures: an impediment to efficient data mining
Whereas the vast majority of the more than 85 000 crystal structures of macromolecules
currently deposited in the Protein Data Bank are of high quality, some suffer from a variety of …
currently deposited in the Protein Data Bank are of high quality, some suffer from a variety of …