Features and development of Coot.
TL;DR: Coot is a molecular-graphics program designed to assist in the building of protein and other macromolecular models and the current state of development and available features are presented.
read more
Abstract: Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and graphics. The software is designed to be easy to learn for novice users, which is achieved by ensuring that tools for common tasks are `discoverable' through familiar user-interface elements (menus and toolbars) or by intuitive behaviour (mouse controls). Recent developments have focused on providing tools for expert users, with customisable key bindings, extensions and an extensive scripting interface. The software is under rapid development, but has already achieved very widespread use within the crystallographic community. The current state of the software is presented, with a description of the facilities available and of some of the underlying methods employed.
read more
Chat with Paper
AI Agents for this Paper
Find similar papers on Google Scholar, PubMed and Arxiv
Write a critical review of this paper
Analyze citations of this paper to find unaddressed research gaps
Citations
Systemic depletion of L-cyst(e)ine with cyst(e)inase increases reactive oxygen species and suppresses tumor growth
Shira L. Cramer,Achinto Saha,Jinyun Liu,Surendar Tadi,Stefano Tiziani,Wupeng Yan,Kendra Triplett,Candice Lamb,Susan E. Alters,Scott W. Rowlinson,Yan Jessie Zhang,Michael J. Keating,Peng Huang,John DiGiovanni,George Georgiou,Everett Stone +15 more
TL;DR: It was observed that enzyme-mediated depletion of the serum L-Cys and CSSC pool suppresses the growth of multiple tumors, yet is very well tolerated for prolonged periods, suggesting that cyst(e)inase represents a safe and effective therapeutic modality for inactivating antioxidant cellular responses in a wide range of malignancies.
Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2
Matthias Thoms,Robert Buschauer,Michael Ameismeier,Lennart Koepke,Timo Denk,Maximilian Hirschenberger,Hanna Kratzat,Manuel Hayn,Timur Mackens-Kiani,Jingdong Cheng,Christina M. Stürzel,Thomas Fröhlich,Otto Berninghausen,Thomas Becker,Frank Kirchhoff,Konstantin M. J. Sparrer,Roland Beckmann +16 more
TL;DR: It is shown that Nsp1 from SARS-CoV-2 binds to 40S and 80S ribosomes, resulting in shutdown of capped mRNA translation both in vitro and in cells, which effectively blocks RIG-I-dependent innate immune responses that would otherwise facilitate clearance of the infection.
460
Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser.
Christopher Kupitz,Shibom Basu,Ingo Grotjohann,Raimund Fromme,Nadia A. Zatsepin,Kimberly N. Rendek,Mark S. Hunter,Mark S. Hunter,Robert L. Shoeman,Thomas A. White,Dingjie Wang,Daniel James,Jay-How Yang,Danielle E. Cobb,Brenda Reeder,Raymond G. Sierra,Haiguang Liu,Anton Barty,Andrew Aquila,Daniel P. DePonte,Richard A. Kirian,Sadia Bari,Jesse J. Bergkamp,Kenneth R. Beyerlein,Michael J. Bogan,Carl Caleman,Tzu-Chiao Chao,Tzu-Chiao Chao,Chelsie E. Conrad,Katherine M. Davis,Holger Fleckenstein,Lorenzo Galli,Stefan P. Hau-Riege,Stephan Kassemeyer,Hartawan Laksmono,Mengning Liang,Lukas Lomb,Stefano Marchesini,Andrew V. Martin,Marc Messerschmidt,Despina Milathianaki,Karol Nass,Alexandra Ros,Shatabdi Roy-Chowdhury,Kevin Schmidt,M. Marvin Seibert,M. Marvin Seibert,Jan Steinbrener,Francesco Stellato,Lifen Yan,Chun Hong Yoon,Thomas A. Moore,Ana L. Moore,Yulia Pushkar,Garth J. Williams,Sébastien Boutet,R. Bruce Doak,Uwe Weierstall,Matthias Frank,Henry N. Chapman,John C. H. Spence,Petra Fromme +61 more
TL;DR: Time resolved experiments on PSII nano/microcrystals from Thermosynechococcus elongatus performed with the recently developed technique of serial femtosecond crystallography provide evidence that PSII undergoes significant conformational changes at the electron acceptor side and at the Mn4CaO5 core of the OEC.
Labeling of active neural circuits in vivo with designed calcium integrators
Benjamin F. Fosque,Yi Sun,Hod Dana,Chao-Tsung Yang,Tomoko Ohyama,Michael R. Tadross,Ronak Patel,Marta Zlatic,Douglas S. Kim,Misha B. Ahrens,Vivek Jayaraman,Loren L. Looger,Eric R. Schreiter +12 more
TL;DR: A fluorescent sensor, CaMPARI, is designed that combines the genetic targetability and quantitative link to neural activity of GECIs with the permanent, large-scale labeling of IEGs, allowing a temporally precise “activity snapshot” of a large tissue volume.
458
The architecture of respiratory supercomplexes
TL;DR: These are the first complete architectures of the dominant, physiologically relevant state of the electron transport chain of mammalian (ovine) supercomplexes determined by cryo-electron microscopy.
458
References
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.
Refinement of macromolecular structures by the maximum-likelihood method.
TL;DR: The likelihood function for macromolecular structures is extended to include prior phase information and experimental standard uncertainties and the results derived are consistently better than those obtained from least-squares refinement.
15.6K
Marching cubes: A high resolution 3D surface construction algorithm
William E. Lorensen,Harvey E. Cline +1 more
- 01 Aug 1987
TL;DR: In this paper, a divide-and-conquer approach is used to generate inter-slice connectivity, and then a case table is created to define triangle topology using linear interpolation.
Improved methods for building protein models in electron density maps and the location of errors in these models.
TL;DR: In this paper, the authors describe strategies and tools that help to alleviate this problem and simplify the model-building process, quantify the goodness of fit of the model on a per-residue basis and locate possible errors in peptide and side-chain conformations.
The Protein Data Bank: a computer-based archival file for macromolecular structures.
Frances C. Bernstein,Thomas F. Koetzle,Graheme J. B. Williams,Edgar F. Meyer,Michael D. Brice,John R. Rodgers,O. Kennard,Takehiko Shimanouchi,Mitsuo Tasumi +8 more
TL;DR: The Protein Data Bank is a computer-based archival file for macromolecular structures that stores in a uniform format atomic co-ordinates and partial bond connectivities, as derived from crystallographic studies.
8.7K
Related Papers (5)
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