Citations
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MASSHA – a graphics system for rigid-body modelling of macromolecular complexes against solution scattering data
Peter V. Konarev,Peter V. Konarev,Maxim V. Petoukhov,Maxim V. Petoukhov,Dmitri I. Svergun,Dmitri I. Svergun +5 more
TL;DR: A program, MASSHA, for three-dimensional rendering and rigid-body refinement of the quaternary structure of macromolecular complexes, which allows display and manipulation of high-resolution atomic structures and low-resolution models represented as smooth envelopes or ensembles of beads.
Journal ArticleDOI
How to do an evaluation: pitfalls and traps
TL;DR: This paper compares a number of docking tools for their performance in cognate re-docking (pose prediction) and/or virtual screening using a variety of ligand-based approaches.
Journal ArticleDOI
The refined structure of human rhinovirus 16 at 2.15 A resolution: implications for the viral life cycle.
Andrea T. Hadfield,Wai-Ming Lee,Rui Zhao,Marcos A. Oliveira,Iwona Minor,Roland R. Rueckert,Michael G. Rossmann +6 more
TL;DR: The observation of a partially occupied hydrophobic pocket in HRV16 forms a missing link between HRV14, which is always observed with no pocket factor in the native form, and rhinovirus 1A and other picornaviruses (e.g. poliovirus, coxsackievirus) which contain pocket factors.
Journal ArticleDOI
A robotic system for crystallizing membrane and soluble proteins in lipidic mesophases.
Vadim Cherezov,A. Peddi,Lalitha Muthusubramaniam,Yuan F. Zheng,Martin Caffrey,Martin Caffrey +5 more
TL;DR: The performance characteristics of the robotic system and the versatility of the crystallization robot in performing vapor-diffusion, microbatch and bicelle crystallizations of membrane and soluble proteins are described.
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New software for statistical analysis of Cambridge Structural Database data
TL;DR: A new piece of software for statistical analysis of geometrical, chemical and crystallographic data within the Cambridge Structural Database System is described, which provides simultaneous visualization of the three-dimensional structural information.
References
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Journal ArticleDOI
The Protein Data Bank
Helen M. Berman,John D. Westbrook,Zukang Feng,Gary L. Gilliland,Talapady N. Bhat,Helge Weissig,Ilya N. Shindyalov,Philip E. Bourne +7 more
TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
Journal ArticleDOI
Crystal structure refinement with SHELXL
TL;DR: New features added to the refinement program SHELXL since 2008 are described and explained.
Journal ArticleDOI
Coot: model-building tools for molecular graphics.
Paul Emsley,Kevin Cowtan +1 more
TL;DR: CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics.
Journal ArticleDOI
PHENIX: a comprehensive Python-based system for macromolecular structure solution
Paul D. Adams,Paul D. Adams,Pavel V. Afonine,Gábor Bunkóczi,Vincent B. Chen,Ian W. Davis,Nathaniel Echols,Jeffrey J. Headd,Li-Wei Hung,Gary J. Kapral,Ralf W. Grosse-Kunstleve,Airlie J. McCoy,Nigel W. Moriarty,Robert D. Oeffner,Randy J. Read,David S. Richardson,Jane S. Richardson,Thomas C. Terwilliger,Peter H. Zwart +18 more
TL;DR: The PHENIX software for macromolecular structure determination is described and its uses and benefits are described.
Journal ArticleDOI
Phaser crystallographic software
Airlie J. McCoy,Ralf W. Grosse-Kunstleve,Paul D. Adams,Martyn Winn,Laurent C. Storoni,Randy J. Read +5 more
TL;DR: A description is given of Phaser-2.1: software for phasing macromolecular crystal structures by molecular replacement and single-wavelength anomalous dispersion phasing.