Citation Information

Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. 

Please acknowledge your use of the Holst group software by citing (for PMG):

    M. Holst and F. Saied, Multigrid solution of the Poisson-Boltzmann equation. J. Comput. Chem., 14 (1993), pp. 105-113. 
    M. Holst and F. Saied, Numerical solution of the nonlinear Poisson-Boltzmann equation: Developing more robust and efficient methods. J. Comput. Chem., 16 (1995), pp. 337-364. 

or for FEtk:

    M. Holst, Adaptive numerical treatment of elliptic systems on manifolds. Advances in Computational Mathematics, 15 (2001), pp. 139-191. 
    R. Bank and M. Holst, A New Paradigm for Parallel Adaptive Meshing Algorithms. SIAM Review, 45 (2003), pp. 291-323.

Zwart, P.H., Langer, G.G. & Lamzin, V.S. (2004) Modelling bound ligands in protein crystal structures. Acta Crystallogr. D60, 2230-2239   Abstract
Cohen, S.X., Morris, R.J., Fernandez, F.J., Jelloul, M. Ben, Kakaris, M., Parthasarathy, V., Lamzin, V.S., Kleywegt, G.J. & Perrakis, A. (2004) Towards complete validated models in the next generation of ARP/wARP. Acta Crystallogr. D60, 2222-2229 Abstract
Morris, R.J., Zwart, P.H., Cohen, S., Fernandez, F.J., Kakaris, M., Kirillova, O., Vonrhein, C., Perrakis, A. & Lamzin, V.S. (2004) Breaking good resolutions with ARP/wARP. J. Synchr. Rad. 11, 56-59 Abstract
Morris, R.J., Perrakis, A. & Lamzin, V.S. (2002) ARP/wARP's model-building algorithms. I. The main chain. Acta Cryst. D58, 968-975 Abstract
Perrakis, A., Harkiolaki, M., Wilson, K.S. & Lamzin, V.S. (2001) ARP/wARP and molecular replacement. Acta Cryst. D57, 1445-1450 Abstract
Lamzin, V.S., Perrakis, A. & Wilson, K.S. (2001) The ARP/WARP suite for automated construction and refinement of protein models. In Int. Tables for Crystallography. Vol. F: Crystallography of biological macromolecules (Rossmann, M.G. & Arnold, E. eds.), Dordrecht, Kluwer Academic Publishers, The Netherlands, pp. 720-722
Lamzin, V.S. & Perrakis, A. (2000) Current state of automated crystallographic data analysis. Nature Struct. Biol. 7, Structural Genomics Supplement, 978-981 Abstract
Perrakis, A., Morris, R.M. & Lamzin, V.S. (1999) Automated protein model building combined with iterative structure refinement. Nature Struct. Biol. 6, 458-463 Abstract
Perrakis, A., Sixma, T.K., Wilson K.S. & Lamzin, V.S. (1997) wARP: improvement and extension of crystallographic phases by weighted averaging of multiple refined dummy atomic models. Acta Cryst. D53, 448-455
Lamzin, V.S. & Wilson, K.S. (1997) Automated refinement for protein crystallography. In Meth. Enz. (Carter, C. & Sweet, B. eds.) 277, 269-305
Lamzin, V.S. & Wilson, K.S. (1993) Automated refinement of protein models. Acta Cryst. D49, 129-147

Research Publications, including scientific papers, films, videotapes and CDs, by the Recipient
Scientist resulting from the use of the Software should cite Professor Arthur Olson, the author of the
Software, and the following publications:
1) Goodsell, D.S. and Olson, A.J. (1990) Automated Docking of Substrates to Proteins by
Simulated Annealing. Proteins: Structure, Function, and Genetics 8:195-202.
2) Morris, G.M., Goodsell, D.S., Huey, R. and Olson, A.J. (1996) Distributed Automated
Docking of Flexible Ligands to Proteins: Parallel Applications of AutoDock 2.4. J.
Computer-Aided Molecular Design 10:293-304.
3) Morris, G.M., Goodsell, D.S., Halliday, R.S., Huey, R., Hart, W.E., Belew, R.K., Olson,
A.J. (1998) Automated docking using Lamarckian genetic algorithm and an empirical
binding free energy function. J. Comp. Chem. 19:1639-1662.

Weeks, C.M., Blessing, R.H., Miller, R., Mungee, R., Potter, S.A.,
Rappleye, J., Smith, G.D., Xu, H. & Furey, W. (2002). Towards automated
protein structure determination: BnP, the SnB-PHASES interface, Z.
Kristallogr. 217, 686-693.

COLLABORATIVE COMPUTATIONAL PROJECT, NUMBER 4, 1994.
"The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst.
D50, 760-763

Recent developments in the PHENIX software for automated
crystallographic structure determination. P.D. Adams, K. Gopal, R.W.
Grosse-Kunstleve, L.-W. Hung, T.R. Ioerger, A.J. McCoy, N.W. Moriarty,
R.K. Pai, R.J. Read, T.D. Romo, J.C. Sacchettini, N.K. Sauter, L.C.
Storoni and T.C. Terwilliger. J. Synchrotron Rad. 11, 53-55 (2004)

CRYSTALLOGRAPHY AND NMR SYSTEM (CNS): A NEW SOFTWARE SYSTEM
FOR MACROMOLECULAR STRUCTURE DETERMINATION". BRUNGER A.T., ADAMS P.D.,
CLORE G.M., DELANO W.L., GROS P., GROSSE-KUNSTLEVE R.W., JIANG J.-S.,
KUSZEWSKI J., NILGES N., PANNU N.S., READ R.J., RICE L.M., SIMONSON T.,
AND WARREN G.L. ACTA CRYST. D54, 905-921 (1998).

You can use this BibTeX database entry (which can be imported into EndNote)... format as you please:

@Article{emsley04:coot,
  author =    {Paul Emsley and Kevin Cowtan},
  title =     {Coot: Model-Building Tools for Molecular Graphics},
  journal =   {Acta Crystallographica Section D - Biological Crystallography},
  year =      2004,
  volume =    60,
  pages  =    2126-2132
}

This information is not yet available

Z. Otwinowski and W. Minor, " Processing of X-ray Diffraction Data Collected in Oscillation Mode ", Methods in Enzymology, Volume 276: 
Macromolecular Crystallography, part A, p.307-326, 1997,C.W. Carter, Jr. & R. M. Sweet, Eds., Academic Press (New York).

"LAFIRE: an automatic refinement program for protein crystallography".
YAO M., ZHOU Y., AND TANAKA I., To be published

This information is not yet available

Per J. Kraulis, "MOLSCRIPT: A Program to Produce Both Detailed and Schematic Plots of Protein Structures", Journal of Applied Crystallography (1991) vol 24, pp 946-950.

The NAMD License Agreement specifies that any reports or published results obtained with NAMD shall acknowledge its use and credit the developers as:

    "NAMD was developed by the Theoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign." 

Any published work which utilizes NAMD shall include the following reference:

    Laxmikant Kalé, Robert Skeel, Milind Bhandarkar, Robert Brunner, Attila Gursoy, Neal Krawetz, James Phillips, Aritomo Shinozaki, Krishnan Varadarajan, and Klaus Schulten. NAMD2: Greater scalability for parallel molecular dynamics. Journal of Computational Physics, 151:283-312, 1999. abstract 

Electronic documents shall include a direct link to the official NAMD page:

    http://www.ks.uiuc.edu/Research/namd/

T.A. Jones, J-Y. Zou, S.W. Cowan & M. Kjeldgaard (1991)
Improved methods for the building of protein models in electron
density maps and the location of errors in these models.
Acta Cryst. A47 110-119.

Acta Cryst. (2004). D60, 432-438. Likelihood-enhanced fast rotation
functions. L. C. Storoni, A. J. McCoy and R. J. Read

Warren L. DeLano "The PyMOL Molecular Graphics System."
DeLano Scientific LLC, San Carlos, CA, USA. http://www.pymol.org

The currently preferred literature reference to RasMol is: Roger Sayle and E. James Milner-White. "RasMol: Biomolecular graphics for all", Trends in Biochemical Sciences (TIBS), September 1995, Vol. 20, No. 9, p. 374.

In addition the best reference for the 2.7 series is: Herbert J. Bernstein, "Recent changes to RasMol, recombining the variants, Trends in Biochemical Sciences (TIBS), September 2000, Vol. 25, No. 9, pp. 453-455.

M. Carson (1997) Ribbons. Methods in Enzymology 277:493-505, R.M. Sweet and C.W. Carter, eds, Academic Press.

C.M. Bruns, I. Hubatsch, M. Ridderström, B. Mannervik, and J.A. Tainer
(1999) Human Glutathione Transferase A4-4 Crystal Structures and
Mutagenesis Reveal the Basis of High Catalytic Efficiency with Toxic
Lipid Peroxidation Products. Journal of Molecular Biology 288(3):
427-439

SHELXL (refinement): Sheldrick, G. M. & Schneider, T. R. (1997). SHELXL:
high resolution refinement. Methods in Enzymology, 277, edited by C. W.
Carter, Jr. & R. M. Sweet, pp. 319–343. San Diego: Academic Press.
SHELXS (direct methods): Sheldrick, G. M. (1990). Phase annealing in
SHELX-90: direct methods for larger structures. Acta Cryst. A46, 467–473.
SHELXS (Patterson): Sheldrick, G. M., Dauter, Z., Wilson, K. S., Hope,
H. & Sieker, L. C. (1993). The application of direct methods and
Patterson interpretation to high-resolution native protein data. Acta
Cryst. D49, 18–23.
SHELXD: Usón, I. & Sheldrick, G. M. (1999). Advances in direct methods
for protein crystallography. Curr. Opinion in Struct. Biol. 9, 643–648.

E. de La Fortelle & G. Bricogne (1997) "Maximum-Likelihood Heavy-Atom
Parameter Refinement for the Multiple Isomorphous Replacement and
Multiwavelength Anomalous Diffraction Methods" Methods in Enzymology 276
472-494. New York: Academic Press.

autoSHARP : the above and
C. Vonrhein, E. Blanc, P. Roversi & G. Bricogne. An Automated Structure
Determination System. in preparation.

1. Please cite the following reference for SnB: Weeks, C.M. &
Miller, R. (1999). The design and implementation of SnB v2.0, J. Appl. Cryst. 32, 120-124.
2. Please cite the following reference for DREAR normalization:
Blessing, R.H. & Smith, G.D. (1999). Difference structure-factor normalization for
heavy-atom or anomalous-scattering substructure determinations, J. Appl. Cryst. 32, 664-670.
3. For Se substructure work utilizing anomalous difference data,
please cite references D3 and D4.

SOLVE references

Terwilliger, T.C. and J. Berendzen. (1999) "Automated MAD and MIR
structure solution". Acta Crystallographica D55, 849-861.

For automated MAD structure determinations, references 1-3, 5 , 6, and
11 are appropriate; for automated MIR structure determinations,
references 1-4 are appropriate.

1. Terwilliger, T. C., Kim, S.-H., and D. Eisenberg. (1987). Generalized
method of determining heavy-atom positions using the difference
Patterson function. Acta Cryst. A43, 1-5.

2. Terwilliger, T. C. and D. Eisenberg. (1983). Unbiased
three-dimensional refinement of heavy-atom parameters by correlation of
origin-removed Patterson functions. Acta Cryst. A39, 813-817.

3. Terwilliger, T. C. and D. Eisenberg. (1987). Isomorphous replacement:
effects of errors on the phase probability distribution. Acta Cryst.
A43, 6-13.

4. Terwilliger, T. C. and J. Berendzen (1996) Correlated phasing of
multiple isomorphous replacement data. Acta Cryst. D52, 749-757.

5. Terwilliger, T. C. (1994). MAD phasing: treatment of dispersive
differences as isomorphous replacement information. Acta Cryst. D50, 17-23.

6. Terwilliger, T. C. (1994) MAD phasing: Bayesian estimates of Fa. Acta
Cryst. D50, 11-16.

7. Terwilliger, T. C. and J. Berendzen (1995). Difference refinement: a
method for estimating differences between related structures. Acta
Cryst. D51, 609-618.

8. Terwilliger, T. C. and Berendzen, J. (1996). Bayesian difference
refinement. Acta Crystallographica section D52, 1004-1011.

9. Terwilliger, T. C. and Berendzen, J. (1996). Bayesian weighting for
macromolecular crsytallographic refinement. Acta Cryst. D52, 743-748.

10. Terwilliger, T. C. and Berendzen, J. (1996). Correlated phasing in
multiple isomorphous replacement. Acta Cryst D52, 749-757.

------------------------------------------------------------------------

RESOLVE references

1. T. C. Terwilliger (1999) "Reciprocal-space solvent flattening,"
Acta Crystallographica D55,1863-1871.
2. T. C. Terwilliger (2000) "Maximum likelihood density
modification," Acta Cryst. D56, 965-972
3. T. C. Terwilliger (2001) "Maximum-likelihood density modification
with pattern recognition of structural motifs" Acta Cryst., D57, 1755-1762
4. T. C. Terwilliger (2001) "Map-likelihood phasing" Acta Cryst.,
D57, 1763-1775
5. Terwilliger, T. C. (2004) Removing model bias in macromolecular
crystallography. (in preparation)
6. Terwilliger, T. C. (2002). Statistical density modification with
non-crystallographic symmetry. Acta Cryst. D58, 2082-2086.
7. Terwilliger, T. C. (2002). Rapid Automatic NCS identification
Using Heavy-Atom Substructures. Acta Cryst. D58, 2213-2215.
8. Terwilliger, T. C. (2002). Automated main-chain model-building by
template-matching and iterative fragment extension. Acta Cryst. D59, 34-44.
9. Terwilliger, T. C. (2002). Automated side-chain model-building and
sequence assignment by template-matching. Acta Cryst. D59, 45-49.
10. Terwilliger, T. C. (2002). Improving atomic models at moderate
resolution by automated iterative model-building and refinement. Acta
Cryst. D59, 1174-1182.
11. Terwilliger, T. C. (2003) Statistical density modification using
local pattern matching. Acta Cryst. D59, 1688-1701.

The user agrees that any reports or published results obtained with  
the Software will acknowledge its use by the appropriate citation as  
follows:

"VMD was developed by the Theoretical and Computational Biophysics Group 
 in the Beckman Institute for Advanced Science and Technology at the 
 University of Illinois at Urbana-Champaign."

Any published work which utilizes VMD shall include the following reference:
"Humphrey, W., Dalke, A. and Schulten, K., `VMD -Visual Molecular   
Dynamics', J. Molecular Graphics, 1996, vol. 14, pp. 33-38."

Electronic documents will include a direct link to the official VMD page  
at  http://www.ks.uiuc.edu/Research/vmd/

Bernal, J.D. 1926 On the interpretation of X-ray, single crystal, rotationphotographs, Proc. Royal Soc. (London) 113A, 117-160.

Bragg, W.L. 1913. Proc. Camb. Phil. Soc. 17:43-?.

Ewald, P.P. 1913. Physikal. Zeit., 14:465-?.

Ewald, P.P. 1913. Physikal. Zeit., 14:1018-?.

Ewald, P.P. 1921. Zeit. f. Krist, 56:129-?.

Open Software Foundation. 1991. "OSF/Motif Programmer's Reference", Prentice Hall, New Jersey.

McRee, D.E. (1992) A visual protein crystallographic software system for X11/XView.
J. Molecular Graphics, Vol.10, pp. 44-46.