Uppsala Software Factory - Literature references
This document contains literature references for O and related
programs from Uppsala, as well as other methodological work.
The references are sorted by year.
Some reprints (PDF files) are available
here.
2003
- Davis, A.M., Teague, S.J. and Kleywegt, G.J. (2003).
Applications and limitations of X-ray crystallographic data in
structure-based ligand and drug design.
Angew. Chem., accepted (to be published in May, 2003).
Discusses limitations in the structure-based design process,
e.g. due to limited accuracy of crystal structures, the inability
to design anything more than ligands, etc.
- Kleywegt, G.J. and Hansson, H. (2003).
Retrieval and validation of structural information.
In "Structural Proteomics", A Edwards, M Sundström &
M Norin, Eds., Marcel Dekker, New York, submitted.
Discusses structural databases available through the
Internet as well as methods and tools for validation of
protein structures by non-experts.
- Kleywegt, G.J., Harris, M.R., Zou, J.Y., Taylor, T.T.,
Wählby, A. & Jones, T.A. (2003).
The Uppsala Electron Density Server (EDS) - a touch of reality.
To be submitted.
Discusses EDS (aimed at a non-expert audience, e.g.
molecular biologists, biochemists, medicinal chemists).
- Novotny, M., Madsen, D. & Kleywegt, G.J. (2003).
An evaluation of protein-fold-comparison servers.
Submitted.
A tough "consumer test" of web-based servers,
including DALI, DEJAVU, and many others.
2002
- Harris, M. and Jones, T.A. (2002).
Xtrack - a web-based crystallographic notebook.
Acta Cryst. D58, 1889-1891.
Xtrack is a web-based database-backed crystallographic notebook
system that allows groups of workers to keep track of
crystallographic project data from the crystallization stage
through to data bank deposition.
(MEDLINE)
(IUCr archive)
- Kleywegt, G.J. and Jones, T.A. (2002).
Homo Crystallographicus - Quo Vadis ?
Structure 10, 465-472.
Discusses developments w.r.t. model quality and
refinement practice during the 1990s.
(Request PDF)
(MEDLINE)
- Madsen, D. and Kleywegt, G.J. (2002).
Interactive motif and fold recognition in protein structures.
J. Appl. Cryst. 35, 137-139.
Discusses improvements in DEJAVU and SPASM, as well
as the web-based servers for these programs.
(Request PDF)
(IUCr archive)
2001
- Kleywegt, G.J., Zou, J.Y., Kjeldgaard, M. and Jones, T.A. (2001).
Around O.
In: "International Tables for Crystallography, Volume F.
Crystallography of Biological Macromolecules" (Rossmann, M.G. and
Arnold, E., Editors). Chapter 17.1, pp. 353-356, 366-367.
Dordrecht: Kluwer Academic Publishers, The Netherlands.
Briefly describes most of the Uppsala programs.
- Kleywegt, G.J. (2001).
Validation of protein crystal structures.
In: "International Tables for Crystallography, Volume F.
Crystallography of Biological Macromolecules" (Rossmann, M.G. and
Arnold, E., Editors). Chapter 21.1, pp. 497-506, 526-528.
Dordrecht: Kluwer Academic Publishers, The Netherlands.
Discusses model errors, quality control and validation.
- Harris, M. and Jones, T.A. (2001). Molray - a web interface between
O and the POV-Ray ray tracer. Acta Cryst D57, 1201-1203.
Discusses the Molray server.
(IUCr archive)
- Read, R.J. and Kleywegt, G.J. (2001).
Density modification: theory and practice.
In: "Methods in Macromolecular Crystallography" (D Turk and
L Johnson, Eds.), IOS Press, Amsterdam, pp. 123-135.
Review of theoretical and practical aspects of
electron-density modification.
2000
- Chen, Y.W., Dodson, E.J. and Kleywegt, G.J. (2000).
Does NMR mean "Not for Molecular Replacement" ? Using NMR-based
search models to solve protein crystal structures.
Structure 8, R213-R220.
Ways & Means review of using multiple (NMR or X-ray)
search models in Molecular Replacement calculations.
(MEDLINE)
(Request PDF)
- Kleywegt, G.J. (2000). Validation of protein crystal structures.
Acta Cryst. D56, 249-265 (Topical Review).
A slightly reworked version of Chapter 21.1 of the Int.
Tables, Volume F.
(IUCr archive)
(MEDLINE)
(Request PDF)
1999
- Kleywegt, G.J. (1999). Experimental assessment of differences
between related protein crystal structures. Acta Cryst. D55,
1878-1884.
Experimental validation of structural differences between
NCS-related molecules and related molecules in different
crystals (COMA/MASKIT, MAPMAN, O, LSQMAN, MOLEMAN2, O2D).
(IUCr archive)
(MEDLINE)
(Tutorial)
(Request PDF)
- Jones, T.A. and Kleywegt, G.J. (1999). CASP3 comparative
modelling evaluation. Proteins: Struct. Funct. Genet. Suppl.
3, 30-46.
Discusses tools used to evaluate the homology modelling
competition results in CASP3 (O, LSQMAN).
(MEDLINE)
(More information)
(Request PDF)
- Kleywegt, G.J. and Jones, T.A. (1999). Software for handling
macromolecular envelopes. Acta Cryst D55, 941-944.
Discusses masks and relevant tools (O, MAMA, COMA, MASKIT).
(IUCr archive)
(MEDLINE)
(Request PDF)
- Kleywegt, G.J. (1999). Recognition of spatial motifs in
protein structures. J Mol Biol 285, 1887-1897.
Discusses algorithm and applications of SPASM (and RIGOR).
(MEDLINE)
(Tutorial)
(Request PDF)
1998
- Kleywegt, G.J. and Jones, T.A. (1998). Databases in protein
crystallography.
Acta Cryst D54, 1119-1131 (CCP4 Proceedings).
Discusses old and new applications of databases in protein
crystallographic model building, refinement, validation, and
analysis. Until I have time to write SBIN up properly,
this paper also serves as an appropriate reference for users
of this package. (NOTE: This paper was originally called
"Old gold retold ... and a few new McNuggets", but this was
a trifle too avant garde for one of the referees ...)
(Preprint)
(IUCr archive)
(MEDLINE)
(Request PDF)
- Kleywegt, G.J. (1998). Déjà-vu all over again.
CCP4 Newsletter on Protein Crystallography 35, 10-12.
Describes SPASM and RIGOR.
(CCP4)
(Web version)
1997
- Kleywegt, G.J. and Jones, T.A. (1997). Template convolution to enhance or detect
structural features in macromolecular electron-density maps.
Acta Cryst D53, 179-185.
This paper describes ESSENS, the real-space convolution program that can be
used to detect helices and strands in experimental maps, prior to any interpretation
(among other things).
(IUCr archive)
(Request PDF)
- Kleywegt, G.J. and Jones, T.A. (1997). Taking the fun out of map interpretation.
CCP4/ESF-EACBM Newsletter on Protein Crystallography 33, 19-21.
Describes some new developments in map interpretation software (ESSENS,
SOLEX, DEJAVU).
(CCP4)
(Web version)
- Jones, T.A. and Kjeldgaard, M. (1997). Electron-density map interpretation.
Meth Enzymol 277, 173-208.
Discusses the use of O to produce the first protein model.
(Ad)
- Kleywegt, G.J. and Jones, T.A. (1997). Model-building and refinement practice.
Meth Enzymol 277, 208-230.
Discusses "good practice" regarding rebuilding and refinement (mentions
O and OOPS).
(Preprint)
(Ad)
- Kleywegt, G.J. and Jones, T.A. (1997). Detecting folding motifs and similarities
in protein structures. Meth Enzymol 277, 525-545.
Discusses DEJAVU, LSQMAN and O's LSQ and YASSPA commands.
(Ad)
- Kleywegt, G.J. (1997). Les amis d'O.
CCP4/ESF-EACBM Newsletter on Protein Crystallography 34, 5-8.
Describes some of the lesser known programs (SOD, O2D, ODBMAN).
(CCP4)
(Web version)
- Kleywegt, G.J. (1997). Validation of protein models from C[alpha]
coordinates alone. J Mol Biol 273, 371-376.
Discusses "CA-Ramachandran plots" as implemented in MOLEMAN
and MOLEMAN2.
(MEDLINE)
(More
information)
(Request PDF)
- Kleywegt, G.J. (1997). HIC-Up: dealing with hetero-compounds.
Protein Data Bank Newsletter 82 (October 1997), 6-7.
Describes the Hetero-compound Information Centre - Uppsala
(using MOLEMAN(2), XPLO2D, HETZE).
(PDB)
- Kleywegt, G.J. and Read, R.J. (1997). Not your average density.
Structure 5, 1557-1569.
Ways & Means review of theoretical and practical aspects of
electron-density averaging.
(MEDLINE)
Request PDF
1996
- Dodson, E., Kleywegt, G.J. and Wilson, K.S. (1996). Report of a workshop on the
use of statistical validators in protein X-ray crystallography.
Acta Cryst D52, 228-234.
Discusses refinement techniques and quality aspects.
(IUCr archive)
(Request PDF)
- Kleywegt, G.J. and Brünger, A.T. (1996). Checking your imagination:
applications of the free R value. Structure 4, 897-904.
A review of applications of Rfree in crystallography.
(MEDLINE)
(Request PDF)
- Kleywegt, G.J. and Jones, T.A. (1996). xdlMAPMAN and xdlDATAMAN - programs for
reformatting, analysis and manipulation of biomacromolecular electron-density
maps and reflection data sets. Acta Cryst D52, 826-828.
Describes CCP4-versions of MAPMAN and DATAMAN (part of RAVE).
(IUCr archive)
(Request PDF)
- Kleywegt, G.J. and Jones, T.A. (1996). Efficient rebuilding of protein structures.
Acta Cryst D52, 829-832.
Describes the use of OOPS.
(IUCr archive)
(Request PDF)
- Kleywegt, G.J. and Jones, T.A. (1996). Phi/psi-chology: Ramachandran
revisited. Structure 4, 1395-1400.
Describes the new definition of core and non-core areas of the
Ramachandran plot, as used by O, LSQMAN, OOPS, and MOLEMAN(2).
(MEDLINE)
(More
information)
(Request PDF)
- Kleywegt, G.J. (1996). Use of non-crystallographic symmetry in protein structure
refinement. Acta Cryst D52, 842-857.
Analysis of differences between molecules related by non-crystallographic
symmetry. The analysis was done with LSQMAN; the resulting "quality database"
can be queried with QDB.
(IUCr archive)
(Request PDF)
- Kleywegt, G.J. (1996). Making the most of your search model. CCP4/ESF-EACBM
Newsletter on Protein Crystallography 32, 32-36.
Describes methods and programs that may be useful to make better search
models for difficult molecular replacement cases (MOLEMAN2, LSQMAN, SEAMAN,
XPLO2D, MAPMAN, PACMAN, RAVE).
(CCP4)
(Web version)
- Zou, J.Y. and Jones, T.A. (1996). Towards the automatic interpretation of
macromolecular electron-density maps: qualitative and quantitative matching
of protein sequence to map. Acta Cryst D52, 833-841.
Describes an automated method in O to match sequence to density.
(IUCr archive)
1995
- Harel, M., Kleywegt, G.J., Ravelli, R.B.G., Silman, I. and Sussman, J.L. (1995).
Crystal structure of an acetylcholinesterase-fasciculin complex: interaction of
a three-fingered toxin from snake venom with its target. Structure 3,
1355-1366.
The first application of ESSENS for "phased molecular replacement".
Also the first application of SPASM to look for small motifs of main-
and side-chains in the PDB.
(MEDLINE)
- Kleywegt, G.J. and Jones, T.A. (1995). Where freedom is given, liberties are
taken. Structure 3, 535-540.
Use (and abuse) and analysis of non-crystallographic symmetry in protein
structure refinement (LSQMAN).
(MEDLINE)
- Kleywegt, G.J. and Jones, T.A. (1995). Braille for pugilists. In "Making the
Most of Your Model", edited by W.N. Hunter, J.M. Thornton and S. Bailey. SERC
Daresbury Laboratory, Warrington, pp. 11-24.
Discusses assessing the quality of protein models, including the use of
some of the tools in O.
(Web
version)
- Kleywegt, G.J. (1995). Dictionaries for heteros. CCP4/ESF-EACBM Newsletter
on Protein Crystallography 31, 45-50.
Describes the use of XPLO2D to make X-PLOR dictionaries, and of MOLEMAN to
make O dictionaries for small hetero-compounds.
(Web version)
1994
- Jones, T.A. and Kjeldgaard, M. (1994). Making the first trace with O. In "From
First Map to Final Model", edited by S. Bailey, R. Hubbard and D. Waller. SERC
Daresbury Laboratory, Warrington, pp. 1-13.
Describes the use of O in the practice of chain-tracing.
- Kleywegt, G.J. and Jones, T.A. (1994). Detection, delineation, measurement and
display of cavities in macromolecular structures. Acta Cryst D50, 178-185.
Describes algorithm and applications of VOIDOO.
(IUCr archive)
(Request PDF)
- Kleywegt, G.J. and Jones, T.A. (1994). Halloween ... masks and bones. In "From
First Map to Final Model", edited by S. Bailey, R. Hubbard and D. Waller. SERC
Daresbury Laboratory, Warrington, pp. 59-66.
The first part describes the use of MAMA for creating and improving masks;
the second part outlines the use of DEJAVU when only a rough skeleton is
available to look for proteins with similar fold in the PDB.
(Web
version)
- Kleywegt, G.J., Bergfors, T., Senn, H., Le Motte, P., Gsell, B., Shudo, K. and
Jones, T.A. (1994). Crystal structures of cellular retinoic acid binding proteins I
and II in complex with all-trans-retinoic acid and a synthetic retinoid. Structure
2, 1241-1258.
Introduces the use of Rfree to estimate coordinate errors from Luzzati plots.
(Also a tough molecular replacement and refinement case.)
(MEDLINE)
- Kleywegt, G.J. and Jones, T.A. (1994). A super position. CCP4/ESF-EACBM Newsletter
on Protein Crystallography 31, 9-14.
Describes the use of LSQMAN to superimpose molecules.
(Web version)
- Kleywegt, G.J. and Jones, T.A. (1994). OOPS-a-daisy. CCP4/ESF-EACBM Newsletter on
Protein Crystallography 30, 20-24.
Describes the use of OOPS.
(Web version)
- Zou, J.Y. and Mowbray, S.L. (1994). An evaluation of the use of databases
in protein structure refinement. Acta Cryst D50, 237-249.
Evaluation of O's database tools for model-building and error-checking
purposes.
(IUCr archive)
1993
- Kleywegt, G.J. and Jones, T.A. (1993). Biomacromolecular speleology. CCP4/ESF-EACBM
Newsletter on Protein Crystallography 29, 26-28.
Describes the use of VOIDOO to detect cavities.
(Web version)
- Kleywegt, G.J. and Jones, T.A. (1993). Masks made easy. CCP4/ESF-EACBM Newsletter
on Protein Crystallography 28, 56-59.
Describes the use of MAMA to create and improve masks.
(Web version)
1992
- Jones, T.A. (1992). A, yaap, asap, @#*? A set of averaging programs. In
"Molecular Replacement", edited by E.J. Dodson, S. Gover and W. Wolf.
SERC Daresbury Laboratory, Warrington, pp. 91-105.
This paper describes the A set of programs which formed the basis for RAVE.
1991
- Jones, T.A., Zou, J.Y., Cowan, S.W. and Kjeldgaard, M. (1991). Improved methods
for building protein models in electron density maps and the location of errors
in these models. Acta Cryst A47, 110-119.
The O reference.
(IUCr archive)
1990
- Brändén, C.I. and Jones, T.A. (1990). Between objectivity and
subjectivity. Nature 343, 687-689.
Describes some of the errors that can occur during model-building in
electron-density maps, and the use of real-space fits to help detect
trouble spots (O).
- Jones, T.A., Bergdoll, M. and Kjeldgaard, M. (1990). O: a macromolecular
modelling environment. 1. An overview. In "Molecular Modelling", edited
by S. Ealick and C.E. Bugg. Springer, New York, pp. ?-?.
Introduction to O, in particular about the program's design and least-squares
fitting of two molecules.
1987
- Kraulis, P.J. and Jones, T.A. (1987). Determination of three-dimensional protein
structures from nuclear magnetic resonance data using fragments of known structures.
Proteins 2, 188-201.
Describes a different approach to determine structures from NMR data, using
a database approach.
(MEDLINE)
1986
- Jones, T.A. and Thirup, S. (1986). Using known substructures in protein model
building and crystallography. EMBO J 5, 819-822.
Introduces the use of databases to build models (FRODO, O).
(MEDLINE)
1985
- Jones, T.A. (1985). Interactive computer graphics: FRODO.
Meth Enzymol 115, 157-171.
Another FRODO reference.
(MEDLINE)
1984
- Jones, T.A. and Liljas, L. (1984). Crystallographic refinement of macromolecules
having non-crystallographic symmetry. Acta Cryst A40, 50-57.
Describes the use of averaging and real-space refinement for virus structures
(FRODO).
(IUCr archive)
1982
- Jones, T.A. (1982). ??? In "Computational Crystallography",
edited by D. Sayre. Clarendon Press, Oxford, pp. 303 - ?.
More about FRODO.
1978
- Jones, T.A. (1978). A graphics model building and refinement system for
macromolecules. J Appl Cryst 11, 268-272.
The original FRODO reference.
(IUCr archive)
Latest update at 7 March, 2003.
