Mark Gerstein's Publications

[01]
N Fisch, A Kritz & M Gerstein (1987). "Inverse Problem for Synchrotron Radiation in the Presence of Noise," Proceedings of the Sixth Joint Workshop on Electron Cyclotron Emission and Electron Cyclotron Resonance Heating (ed. A Riviere & A Costley), 23-30 (Oxford, 16-17 September).
[02]
M Gerstein & C H Chothia (1991). "Analysis of Protein Loop Closure: Two Types of Hinges Produce One Motion in Lactate Dehydrogenase," J. Mol. Biol. 220: 133-149.
- [Medline Abstract for 91295198]
[03]
M Gerstein (1992). "A Resolution-Sensitive Procedure for Comparing Protein Surfaces and its Application to the Comparison of Antigen-Combining Sites," Acta Cryst. A48: 271-276.
- [Abstract] [ftp directory with manuscript] [ Talk Abstract]
[04]
I De Baere, L Liu, L Moens, J Van Beeumen, C Gielens, J Richelle, C Trotman, J T Finch, M Gerstein & M F Perutz (1992). "Polar zipper sequence in the high-affinity hemoglobin of Ascaris suum : Amino acid sequence and structural interpretation," Proc. Natl. Acad. Sci. USA 89: 4638-4642.
- [Medline Abstract for 92262495]
[05]
C Chothia & M Gerstein (1992). "Protein Design for Domain Closure," in Muscle as a Machine: Energy Transduction in the Contractile System (editor M Morales), 149-153 (NIH, Bethesda, Maryland, 13-15 April).
[06]
S Subramaniam, M Gerstein, D Oesterhelt & R H Henderson (1993). "Electron diffraction analysis of structural changes in the photocycle of bacteriorhodopsin," EMBO J. 12: 1-8.
- [Medline Abstract for 93154310]
[07]
M Gerstein, G Schulz & C Chothia (1993). "Domain Closure in Adenylate Kinase: Joints on Either Side of Two Helices Close Like Neighboring Fingers," J. Mol. Biol. 229: 494-501.
- [Medline Abstract for 93156056] [Summary Graphic]
[08]
M Gerstein & R M Lynden-Bell (1993). "Simulation of Water around a Model Protein Helix. 1. Two-dimensional Projections of Solvent Structure," J. Phys. Chem. 97: 2982-2991.
[09]
M Suzuki & M Gerstein (1993). "Understanding transcription from X-ray crystal structures: Tactics and Strategy of DNA binding proteins," in New Developments in Transcription Factor Study (editor M Horikoshi, Chugai Medical Company, Tokyo).
[10]
M Gerstein & R M Lynden-Bell (1993). "What is the natural boundary for a protein in solution?" J. Mol. Biol. 230: 641-650.
- [Medline Abstract for 93217998]
[11]
M Gerstein & R M Lynden-Bell (1993). "Simulation of Water around a Model Protein Helix. 2. The Relative Contributions of Packing, Hydrophobicity, and Hydrogen Bonding," J. Phys. Chem. 97: 2991-2999.
- [Abstract]
[12]
M Suzuki, M Gerstein & T Johnson (1993). "An NMR study of the DNA-binding `SPKK' motif and a model for its interaction with DNA," Prot. Eng. 6: 565-574.
- [Medline Abstract for 94052067]
[13]
M Gerstein, A M Lesk, E N Baker, B Anderson, G Norris & C Chothia (1993). "Domain Closure in Lactoferrin: Two Hinges produce a See-saw Motion between Alternative Close-Packed Interfaces," J. Mol. Biol. 234: 357-372.
- [Medline Abstract for 94047086] [Summary Graphic] [ftp directory with many pictures]
[14]
M Gerstein (1994). "Benefits of the Internet," in 51 Reasons: How we use the Internet and What it says about the information superhighway (editors M Stone-Martin & L Breeden, Federation of American Research Networks, Lexington, MA).
- [ Full Text] [About FARNET project]
[15]
M Gerstein, E Sonnhammer & C Chothia (1994). "Volume Changes on Protein Evolution," J. Mol. Biol. 236: 1067-1078.
- [Medline Abstract for 94166074] [Abstract + Full Text] [ftp directory]
[16]
M Gerstein (1994). "Purcell's early work on NMR: Contingency versus Inevitability," Am. J. Phys. 62: 596-601.
- [Abstract + Full Text]
[17]
M Suzuki, D Neuhaus, M Gerstein & S Aimoto (1994). "Solution structure of the DNA binding octapeptide repeat of the K10 gene product," Prot. Eng. 7: 461-470.
- [Medline Abstract for 94301993]
[18]
M Gerstein, A M Lesk & C Chothia (1994). "Structural Mechanisms for Domain Movements," Biochemistry 33: 6739-6749.
- [Medline Abstract for 94263987] [Abstract] [ftp directory with manuscript] [HyperText Database]
[19]
Y Harpaz, M Gerstein & C Chothia (1994). "Volume Changes on Protein Folding," Structure 2: 641-649.
- [Medline Abstract for 95006332]
[20]
R Altman & M Gerstein (1994). "Finding an Average Core Structure: Application to the Globins," Proceedings of the Second International Conferene on Intelligent Systems in Molecular Biology, 19-27 (Menlo Park, CA, AAAI Press, August 14-17).
- [Abstract + Full Text + Pictures]
[21]
M Suzuki, M Gerstein & N Yagi (1994). "The stereochemical basis for DNA recognition by Zn fingers," Nucl. Acid. Res. 22: 3397-3405.
- [Medline Abstract for 94359814]
[22]
M Gerstein, J Tsai & M Levitt (1995). "The volume of atoms on the protein surface: Calculated from simulation, using Voronoi polyhedra," J. Mol. Biol. 249: 955-966.
- [ftp directory with manuscript, talks, programs & data]
[23]
M Suzuki, N Yagi & M Gerstein (1995). "DNA-recognition and superstructure-formation by helix-turn-helix proteins," Prot. Eng. 8: 329-338.
[24]
R Altman, C Hughes & M Gerstein (1995). "Methods for Displaying Macromolecular Structural Uncertainty: Application to the Globins," J. Mol. Graph. 13: 142-152.
- [ Pictures made with program]] [ProteanD program]
[25]
M Suzuki, S Brenner, M Gerstein & N Yagi (1995). "A DNA Recognition Code for Transcription Factors," Prot. Eng. 8: 319-328.
[26]
M Gerstein (1995). "A Protein Motions Database," PDB Quart. Newsletter 73: 2 (July).
- [ftp directory with full text of newsletter] [HyperText Database]
[27]
M Gerstein & R Altman (1995). "Average core structures and variability measures for protein families: Application to the immunoglobulins," J. Mol. Biol. 251: 161-175.
- [ftp directory with full text + other stuff]
[28]
M Gerstein & M Levitt (1995). "Water & Biological Macromolecules," Sci. Am. (in press).
- [Water Simulation Page]
[29]
M Gerstein (1995). "A Protein Motions Database," in Protein Motions (ed. S Subbiah, Austin, TX, RG Landes, in press).
[30]
M Gerstein & R Altman. "A Structurally Invariant Core for the Globins," CABIOS (in press).
- [ftp directory with full text + other stuff]
[31]
M Suzuki & M Gerstein (1995). "The geometry of alpha-helices binding to DNA," Proteins: Struc. Func. Genet. (in press).
[32]
M Gerstein, A Lesk & C Chothia (1995). "Structural Mechanisms for Protein Movements," in Protein Motions (ed. S Subbiah, Austin, TX, RG Landes, in press).

Papers Submitted or In Preparation

10 August 1995 / mbg@hyper.stanford.edu