The Anatomy & Taxonomy of Protein Structure

V. References

Abad-Zapatero C, Abdel-Meguid SS, Johnson JE, Leslie AGW, Rayment I, Rossmann MG, Suck D, Tsukihara T. Structure of southern bean mosaic-virus at 2.8-Å resolution. Nature (1980) 286:33-39.

Abola EE, Ely KR, Edmundson AB. Marked structural differences of the Mcg Bence-Jones dimer in two crystal systems. Biochem (1980) 19:432-439.

Adams MJ, Ford GC, Koekoek R, Lentz PJ, Jr. , McPherson A, Jr. , Rossmann MG, Smiley IE, Schevitz RW, Wonacott AJ. Structure of lactate dehydrogenase at 2-8 Å resolution. Nature (1970) 227:1098-1103.

Adams MJ, Haas DJ, Jeffery BA, McPherson A, Jr. , Mermall HL, Rossmann MG, Schevitz RW, Wonacott AJ. Low resolution study of crystalline L-lactate dehydrogenase. J Mol Biol (1969) 41:159-188.

Adman ET, Sieker LC, Jensen LH. Structure of a bacterial ferredoxin. J Biol Chem (1973) 248:3987-3996.

Adman ET, Stenkamp RE, Sieker LC, Jensen LH. A crystallographic model for azurin at 3Å resolution. J Mol Biol (1978) 123:35-47.

Almassy RJ, Dickerson RE. Pseudomonas cytochrome c551 at 2.0 Å resolution: enlargement of the cytochrome c family. Proc Nat Acad Sci USA (1978) 75:2674-2678.

Anderson CM, McDonald RC, Steitz TA. Sequencing a protein by x-ray crystallography. I. Interpretation of yeast hexokinase B at 2.5 Å resolution by model building. J Mol Biol (1978) 123:1-13.

Anderson CM, Zucker FH, Steitz TA. Space-filling models of kinase clefts and conformation changes. Science (1979) 204:375-380.

Andreeva NS, Gustchina AE. On the supersecondary structure of acid proteases. Biochemical & Biophysical Research Communications (1979) 87:32-42.

Anfinsen CB. The formation and stabilization of protein structure. Biochem J (1972) 128:737-749.

Anfinsen CB, Cuatrecasas P, Taniuchi H. Staphylococcal Nuclease, Chemical Properties and Catalysis. In: Boyer PD, editor. The Enzymes. 3rd ed. Volume 4. New York: Academic Press; 1971. p 177-204.

Anfinsen CB, Scheraga HA. Experimental and theoretical aspects of protein folding. Adv Prot Chem (1975) 29:205-300.

Argos P, Rossmann MG. Structural comparisons of heme binding proteins. Biochem (1979) 18:4951-4960.

Argos P, Rossmann MG, Johnson JE. A four-helical super-secondary structure. Biochemical & Biophysical Research Communications (1977) 75:83-86.

Arnone AA, Bier CJ, Cotton FA, Day VW, Hazen EE, Jr., Richardson DC, Richardson JS, Yonath A. A High Resolution Structure of an Inhibitor Complex of the Extracellular Nuclease of Staphylococcus aureus: I. Experimental Procedures and Chain Tracing. J Biol Chem (1971) 246:2302-2316.

Astbury WT. Some problems in the X-ray analysis of the structure of animal hairs and other protein fibers. Trans Faraday Soc (1933) 29:193.

Astbury WT, Bell FO. Nature of the intramolecular fold in alpha-keratin and alpha-myosin. Nature (1941) 147:696-699.

Baker EN. Structure of actinidin, after refinement at 1.7 Å resolution. J Mol Biol (1980) 141:441-484.

Banks RD, Blake CCF, Evans PR, Haser R, Rice DW, Hardy GW, Merrett M, Phillips AW. Sequence, structure and activity of phosphoglycerate kinase: a possible hinge-bending enzyme. Nature (1979) 279:773-777.

Banner DW, Bloomer AC, Petsko GA, Phillips DC, Pogson CI, Wilson IA, Corran PH, Furth AJ, Milman JD, Offord RE, Priddle JD, Waley SG. Structure of chicken muscle triose phosphate isomerase determined crystallographically at 2.5 angstrom resolution using amino acid sequence data. Nature (1975) 255:609-614.

Banyard SH, Stammers DK, Harrison PM. Electron density map of apoferritin at 2.8-Å resolution. Nature (1978) 271:282-284.

Bennett WS, Jr., Steitz TA. Glucose-induced conformational change in yeast hexokinase. Proc Nat Acad Sci USA (1978) 75:4848-4852.

Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Research (2000) 28:235-242.

Bhat TN, Sasisekharan V, Vijayan M. An Analysis of Side-Chain Conformation in Proteins. Int J Pept Prot Res (1979) 13:170-184.

Birktoft JJ, Blow DM. Structure of crystalline -chymotrypsin. V. The atomic structure of tosyl- -chymotrypsin at 2 Å resolution. J Mol Biol (1972) 68:187-240.

Blake CCF, Geisow MJ, Oatley SJ, Rérat B, Rérat C. Structure of prealbumin: secondary, tertiary and quaternary interactions determined by Fourier refinement at 1.8 Å. J Mol Biol (1978) 121:339-356.

Blake CCF, Mair GA, North ACT, Phillips DC, Sarma VR. On the conformation of the hen egg-white lysozyme molecule. Proceedings of the Royal Society of London - Series B: Biological Sciences (1967) 167:365-377.

Blake CCF, Oatley SJ. Protein-DNA and protein-hormone interactions in prealbumin: a model of the thyroid hormone nuclear receptor? Nature (1977) 268:115-120.

Bloomer A, C. , Champness JN, Bricogne G, Staden R, Klug A. Protein disk of tobacco mosaic-virus at 2.8-Å resolution showing interactions within and between subunits. Nature (1978) 276:362-368.

Blow DM, Birktoft JJ, Hartley BS. Role of a buried acid group in the mechanism of action of chymotrypsin. Nature (1969) 221:337-340.

Blow DM, Irwin MJ, Nyborg J. The peptide chain of tyrosyl tRNA synthetase: no evidence for a super-secondary structure of four alpha-helices. Biochemical & Biophysical Research Communications (1977) 76:728-734.

Blundell TL, Dodson GG, Hodgkin DC, Mercola DA. Insulin. The Structure In The Crystal And Its Reflection In Chemistry And Biology. Adv Prot Chem (1972) 26:279-402.

Blundell TL, Lindley P, Miller L, Moss D, Slingsby C, Tickle I, Turnell B, Wistow G. The molecular structure and stability of the eye lens: x-ray analysis of -crystallin II. Nature (1981) 289:771-777.

Brahms S, Brahms J. Determination of protein secondary structure in solution by vacuum ultraviolet circular dichroism. J Mol Biol (1980) 138:149-178.

Brandts JF, Brennan M, Lin LN. Unfolding and refolding occur much faster for a proline-free proteins than for most proline-containing proteins. Proc Nat Acad Sci USA (1977) 74:4178-4181.

Brandts JF, Halvorson HR, Brennan M. Consideration of the Possibility that the slow step in protein denaturation reactions is due to cis-trans isomerism of proline residues. Biochem (1975) 14:4953-4963.

Brayer GD, Delbaere LTJ, James MNG. Molecular structure of crystalline Streptomyces griseus protease A at 2.8 Å resolution. II. Molecular conformation, comparison with alpha-chymotrypsin and active-site geometry. J Mol Biol (1978) 124:261-283.

Brown KG, Erfurth SC, Small EW, Peticolas WL. Conformationally dependent low-frequency motions of proteins by laser Raman spectroscopy. Proc Nat Acad Sci USA (1972) 69:1467-1469.

Buehner M, Ford GC, Olsen KW, Moras D, Rossman MG. Three-dimensional structure of D-glyceraldehyde-3-phosphate dehydrogenase. J Mol Biol (1974) 90:25-49.

Burnett RM, Darling GD, Kendall DS, LeQuesne ME, Mayhew SG, Smith WW, Ludwig ML. The structure of the oxidized form of clostridial flavodoxin at 1.9-Å resolution. J Biol Chem (1974) 249:4383-4392.

Butler PJG, Klug A. The assembly of a virus. Sci Am (1978) 239:62-69.

Campbell JW, Watson HC, Hodgson GI. Structure of yeast phosphoglycerate mutase. Nature (1974) 250:301-303.

Carter CW, Jr. New stereochemical analogies between iron-sulfur electron transport proteins. J Biol Chem (1977) 252:7802-7811.

Carter CW, Jr. , Kraut J, Freer ST, Xuong N-H, Alden RA, Bartsch RG. Two-Angstrom crystal structure of oxidized Chromatium high potential iron protein. J Biol Chem (1974) 249:4212-4225.

Cavanagh, J, Fairbrother, W, Palmer, AG III, Skelton, N. Protein NMR Spectroscopy: Principles and Practice, 2nd edition. (2006) Academic Press, San Diego.

Chambers JL, Stroud, RM. Acurracy of Refined Protein Structures - Comparison of 2 Independently Refined Models of Bovine Trypsin. Acta Cryst (1979) B35:1861-1874.

Champness JN, Bloomer AC, Bricogne G, Butler PJG, Klug A. The structure of the protein disk of tobacco mosaic virus to 5Å resolution. Nature (1976) 259:20-24.

Chandrasekaran R, Ramachandran GN. Studies on the Conformation of Amino Acids XI. Analysis of the Observed Side Group Conformations in Proteins. Int J Prot Res II (1970) 2:223-233.

Chauvin C, Witz J, Jacrot B. Structure of the tomato bushy stunt virus: a model for protein-RNA interaction. J Mol Biol (1978) 124:641-651.

Chirgadze YN, Nevskaya NA. Infrared spectra and resonance interaction of amide-I vibration of the parallel-chain pleated sheets. Biopolymers (1976) 15:627-636.

Chothia C. Conformation of twisted beta-pleated sheets in proteins. J Mol Biol (1973) 75:295-302.

Chothia C, Levitt M, Richardson DC. Structure of proteins: packing of alpha-helices and pleated sheets. Proc Nat Acad Sci USA (1977) 74:4130-4134.

Chou PY, Fasman GD. Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins. Biochem 1974a; 13:211-221.

Chou PY, Fasman GD. Prediction of protein conformation. Biochem 1974b; 13:222-245.

Chou PY, Fasman GD. Beta-turns in proteins. J Mol Biol (1977) 115:135-175.

Clegg GA, Stansfield RFD, Bourne PE, Harrison PM. Helix packing and subunit conformation in horse spleen apoferritin. Nature (1980) 288:298-300.

Cohen FE, Sternberg MJE, Taylor WR. Analysis and prediction of protein beta-sheet structures by a combinatorial approach. Nature (1980) 285:378-382.

Colman PM, Deisenhofer J, Huber R. Structure of the human antibody molecule Kol (immunoglobulin G1): an electron density map at 5 Å resolution. J Mol Biol (1976) 100:257-278.

Colman PM, Freeman HC, Guss JM, Murata M, Norris VA, Ramshaw JAM, Venkatappa MP. X-Ray Crystal-Structure Analysis of Plastocyanin at 2.7Å Resolution. Nature (1978) 272:319-324.

Colman PM, Jansonius JN, Matthews BW. The structure of thermolysin: an electron density map at 2-3 Å resolution. J Mol Biol (1972) 70:701-724.

Cook DA. The relation between amino acid sequence and protein conformation. J Mol Biol (1967) 29:167-171.

Craik CS, Buchman SR, Beychok S. Characterization of globin domains: heme binding to the central exon product. Proc Nat Acad Sci USA (1980) 77:1384-1388.

Crawford JL, Lipscomb WN, Schellman CG. The reverse turn as a polypeptide conformation in globular proteins. Proc Nat Acad Sci USA (1973) 70:538-542.

Creighton TE. Conformational restrictions on the pathway of folding and unfolding of the pancreatic trypsin inhibitor. J Mol Biol 1977a; 113:275-293.

Creighton TE. Energetics of folding and unfolding of pancreatic trypsin inhibitor. J Mol Biol 1977b; 113:295-312.

Creighton TE. Effects of urea and guanidine-HCl on the folding and unfolding of pancreatic trypsin inhibitor. J Mol Biol 1977c; 113:313-328.

Creighton TE. Kinetics of refolding of reduced ribonuclease. J Mol Biol 1977d; 113:329-341.

Crick FHC. The packing of alpha-helices: simple coiled-coils. Acta Cryst (1953) A6:689-697.

Crippen GM. The tree structural organization of proteins. J Mol Biol (1978) 126:315-332.

Crippen GM, Kuntz ID. A survey of atom packing in globular proteins. International Journal of Peptide & Protein Research (1978) 12:47-56.

Cunningham BA, Hemperly JJ, Hopp TP, Edelman GM. Favin Versus Concanavalin A: Circularly Permuted Amino Acid Sequences. Proc Nat Acad Sci USA (1979) 76:3218-3222.

Davies DR. A correlation between amino acid composition and protein structure. J Mol Biol (1964) 9:605-609.

Dayhoff MO, Barker WC. Mechanisms in molecular evolution: Examples. In: Dayhoff MO, editor. Atlas of Protein Sequence and Structure. Volume 5. Silver Spring, MD: National Biomedical Research Foundation; 1972. p 41-45.

Deisenhofer J, Jones TA, Huber R, Sjodahl J, Sjoquist J. Crystallization, Crystal-Structure Analysis and Atomic Model of Complex Formed by a Human FC Fragment and Fragment-B of Protein-A from

Deisenhofer J, Steigemann W. Crystallographic refinement of the structure of bovine pancreatic trypsin inhibitor at l.5 Å resolution. Acta Cryst (1975) B31:238-250.

Delbaere LTJ, Hutcheon WLB, James MNG, Thiessen WE. Tertiary structural differences between microbial serine proteases and pancreatic serine enzymes. Nature (1975) 257:758-763.

Dickerson RE, Geis I. Chapter 2. The Structure and Action of Proteins. Menlo Park, Calif.: Benjamin/Cummings Publishing Co.; 1969.

Dijkstra BW, Drenth J, Kalk K, Vandermaelen PJ. Three-dimensional structure and disulfide bond connections in bovine pancreatic phospholipase A2. J Mol Biol (1978) 124:53-60.

Doig AJ, Baldwin RL. N- and C-capping preferences for all 20 amino acids in α-helical peptides. Protein Sci. (1995) 4:1325-1336.

Drenth J, Jansonius JN, Koekoek R, Wolthers BG. The structure of papain. Adv Prot Chem (1971) 25:79-115.

Drenth J, Low BW, Richardson JS, Wright CS. The Toxin-Agglutinin Fold: A New Group of Small Protein Structures Organized Around a Four-Disulfide Core. J Biol Chem (1980) 255:2652-2655.

Dunbrack, Jr. RL. Rotamer libraries in the 21st century. Current Opinion in Structural Biology (2002) 12:431-440.

Edelman GM, Gall WE. The antibody problem. Annual Review of Biochemistry (1969) 38:415-466.

Edsall JT, Otvos JW, Rich A. Raman Spectra of Amino Acids and Related Compounds. VII. Glycylglycine, Cysteine, Cystine and Other Amino Acids. J Am Chem Soc (1950) 72:474 - 477.

Efimov AV. Stereochemistry of the packing of alpha-spirals and beta-structure into a compact globule (Russian). Dokl Akad Nauk SSSR (1977) 235:699-702.

Efimov AV. Packing of alpha-helices in globular proteins. Layer-structure of globin hydrophobic cores. J Mol Biol (1979) 134:23-40.

Eklund H, Brändén C-I. Structural differences between apo- and holoenzyme of horse liver alcohol dehydrogenase. J Biol Chem (1979) 254:3458-3461.

Eklund H, Nordström B, Zeppezauer E, Söderlund G, Ohlsson I, Boiwe T, Söderberg B-O, Tapia O, Brändén C-I, Å. Å. Three-dimensional structure of horse liver alcohol dehydrogenase at 2-4 A resolution. J Mol Biol (1976) 102:27-59.

Engelman DM, Henderson R, McLachlan AD, Wallace BA. Path of the polypeptide in bacteriorhodopsin. Proc Nat Acad Sci USA (1980) 77:2023-2027.

Engh RA, Huber R. Accurate Bond and Angle Parameters for X-ray Protein Structure Refinement. Acta Crystallographica (1991) Section A, 47:392-400.

Engh, RA and Huber, R. Structure quality and target parameters. Internat Tables for Cryst F (2001) chap. 18.3: 382-392, Kluwer Academic Publishers, Dordrecht.

Epp O, Colman P, Fehlhammer H, Bode W, Schiffer M, Huber R, Palm W. Crystal and molecular structure of a dimer composed of the variable portions of the Bence-Jones protein REI. Eur J Biochem (1974) 45:513-524.

Epp O, Lattman EE, Schiffer M, Huber R, Palm W. The Molecular Structure of a Dimer Composed of the Variable Portions of the Bence-Jones Protein REI Refined at 2.0-Å Resolution. Biochem (1975) 14:4943-4952.

Feldmann RJ. Atlas of Macromolecular Structure on Microfiche. Rockville, Maryland: Tracor-Jitco; 1977.

Finkelstein AV, Ptitsyn OB. A theory of protein molecule self-organization. IV. Helical and irregular local structures of unfolded protein chains. J Mol Biol (1976) 103:15-24.

Fisher WR, Taniuchi H, Anfinsen CB. On the role of heme in the formation of the structure of cytochrome c. J Biol Chem (1973) 248:3188-3195.

Ford GC, Eichele G, Jansonius JN. Three-dimensional structure of a pyridoxal-phosphate-dependent enzyme, mitochondrial aspartate aminotransferase. Proc Nat Acad Sci USA (1980) 77:2559-2563.

Genzel L, Keilmann F, Martin TP, Winterling G, Yacoby Y, Fröhlich H, Makinen MW. Low-frequency Raman spectra of lysozyme. Biopolymers (1976) 15:219-225.

Gernert, KM, Surles, MC, LaBean, TH, Richardson, JS, Richardson, DC. The Alacoil: A very tight, antiparallel coiled-coil of helices. Protein Sci (1995) 4: 2252-2260.

Ghelis C, Tempete-Gaillourdet M, Yon JM. The folding of pancreatic elastase: independent domain refolding and inter-domain interaction. Biochemical & Biophysical Research Communications (1978) 84:31-36.

Gratzer WB, Beaven GH. Relation between conformation and association state. A study of the association equilibrium of glucagon. J Biol Chem (1969) 244:6675-6679.

Grosse R, Malur J, Meiske W, Repke KRH. Statistical behaviour and suitability of protein-derived circular dichroic-basis spectra for the determination of globular protein conformation. Biochimica et Biophysica Acta (1974) 359:33-46.

Guzzo AV. The influence of amino-acid sequence on protein structure. Biophys J (1965) 5:809-822.

Hagler AT, Moult J. Computer simulation of the solvent structure around biological macromolecules. Nature (1978) 272:222-226.

Harper, ET, Rose GD. Helix stop signals in proteins and peptides: the capping box. Biochemistry (1993) 32: 7605-7609.

Harrison SC, Olson AJ, Schutt CE, Winkler FK, Bricogne G. Tomato Bushy Stunt Virus at 2.9-Å Resolution. Nature (1978) 276:368-373.

Haser R, Pierrot M, Frey M, Payan F, Astier JP, Bruschi M, Legall J. Structure and Sequence of the Multihaem Cytochrome-C3. Nature (1979) 282:806-810.

Henderson R, Unwin PNT. Three-dimensional model of purple membrane obtained by electron microscopy. Nature (1975) 257:28-32.

Hendrickson WA, Klippenstein GL, Ward KB. Tertiary structure of myohemerythrin at low resolution. Proc Nat Acad Sci USA (1975) 72:2160-2164.

Hendrickson WA, Love WE. Structure of lamprey haemoglobin. Nature (1971) 232:197-203.

Hendrickson WA, Teeter MM. Structure of the Hydrophobic Protein Crambin Determined Directly from the Anomalous Scattering of Sulphur. Nature (1981) 290:107-113.

Hendrickson WA, Ward KB. Pseudosymmetry in the structure of myohemerythrin. J Biol Chem (1977) 252:3012-3018.

Hill E, Tsernoglou D, Webb L, Banaszak LJ. Polypeptide conformation of cytoplasmic malate dehydrogenase from an electron density map at 3.0 angstrom resolution. J Mol Biol (1972) 72:577-589.

Hol WG, van Duijnen PT, Berendsen HJ. The alpha-helix dipole and the properties of proteins. Nature (1978) 273:443-446.

Holbrook SR, Sussman JL, Warrant RW, Kim S-H. Crystal structure of yeast phenylalanine transfer RNA. II. Structural features and functional implications. J Mol Biol (1978) 123:631-660.

Holm, L and Sander, C. Protein structure comparison by alignment of distance matrices. J Mol Biol (1993) 233: 123-138.

Holmgren A, Söderberg B-O, Eklund H, Brändèn C-I. Three-dimensional structure of Escherichia coli thioredoxin-S2 to 2.8 A resolution. Proc Nat Acad Sci USA (1975) 72:2305-2309.

Honig B, Ray A, Levinthal C. Conformational flexibility and protein folding: rigid structural fragments connected by flexible joints in subtilisin BPN. Proc Nat Acad Sci USA (1976) 73:1974-1978.

Huber R, Deisenhofer J, Colman PM, Matsushima M, Palm W. Crystallographic structure studies of an IgG molecule and an Fc fragment. Nature (1976) 264:415-420.

Hu H, Elstner M, Hermans L. Comparison of a QM/MM Force Field and Molecular Mechanics Force Fields in Simulations of Alanine and Glycine “Dipeptides” (Ace-Ala-Nme and Ace-Gly-Nme) in Water in Relation to the Problem of Modeling the Unfolded Peptide Backbone in Solution. Proteins: Structure, Function and Genetics (2003) 50:451-463.

Huber R, Kukla D, Bode W, Schwager P, Bartels K, Deisenhofer J, Steigemann W. Structure of the complex formed by bovine trypsin and bovine pancreatic trypsin inhibitor. II. Crystallographic refinement at 1.9 A resolution. J Mol Biol (1974) 89:73-101.

Huber R, Kukla D, Ruhlmann A, Steigemann W. Pancreatic trypsin inhibitor (Kunitz). I. Structure and function. Cold Spring Harbor Symp Quant Biol (1972) 36:141-148.

Huber R, Steigemann W. Two cis-prolines in the Bence-Jones protein Rei and the cis-pro-bend. FEBS Lett (1974) 48:235-237.

Imoto T, Johnson LM, North ACT, Phillips DC, Rupley JA. Vertebrate lysozymes. In: Boyer PD, editor. The Enzymes. Volume 7. New York: Academic Press; 1972. p 665-868.

Irwin MJ, Nyborg J, Reid BR, Blow DM. The crystal structure of tyrosyl-transfer RNA synthetase at 2-7Å resolution. J Mol Biol (1976) 105:577-586.

Isogai Y, Némethy G, Rackovsky S, Leach SJ, Scheraga HA. Characterization of multiple bends in proteins. Biopolymers (1980) 19:1183-1210.

IUPAC-IUB. Commission on Biochemical Nomenclature: Abbreviations and Symbols for the Description of the Conformation of Polypeptide Chains. JMB (1970) 52:1-17.

Janin J, Wodak S, Levitt M, Maigret B. Conformation of Amino Acid Side-chains in Proteins. J Mol Biol (1978) 125:357-386.

Kapp GT, Richardson JS, Oas TG. Kinetic Role of Helix Caps in Protein Folding is Context-Dependent. Biochemistry (2004) 43: 3814-3823.

Karplus PA. Experimentally observed conformation-dependent geometry and hidden strain in proteins. Prot. Sci. (1996) 5:1406-1420.

Karplus, K, Barrett, C, Hughey, R. Hidden Markov models for detecting remote protein homologies. Bioinformatics (1998) 22: 2577-2637.

Kauzmann W. Factors in the interpretation of protein denaturation. Adv Prot Chem (1959) 14:1-64.

Kendrew JC, Bodo G, Dintzis HM, Parrish RG, Wyckoff H, Phillips DC. A three-dimensional model of the myoglobin molecule obtained by X-ray analysis. Nature (1958) 181:662-666.

Kendrew JC, Dickerson RE, Strandberg BE, Hart RG, Davies DR, Phillips DC, Shore VC. Structure of Myoglobin: a three-dimensional Fourier synthesis at 2Å resolution. Nature (1960) 185:422-427.

Kendrew JC, Watson HC, Strandberg BE, Dickerson RE, Phillips DC, Shore VC. A Partial Determination by X-ray Methods, and its Correlation with Chemical Data. Nature (1961) 190:666-670.

Kleywegt GJ. Experimental assessment of differences between related protein crystal structures. Acta Cryst. D (1999) 55:1878-1884.

Klis WA, Siemion IZ. Conformation of disulfide bridges in peptides with pepsin partial sequences. International Journal of Peptide & Protein Research (1978) 12:103-113.

Klotz IM, Langerman NR, Darnall DW. Quaternary structure of proteins. Annual Review of Biochemistry (1970) 39:25-62.

Ko BPN, Yazgan A, Yeagle PL, Lottich SC, Henkens RW. Kinetics and mechanism of refolding of bovine carbonic anhydrase. A probe study of the formation of the active site. Biochem (1977) 16:1720-1725.

Korszun ZR, Salemme FR. Structure of cytochrome c555 of Chlorobium thiosulfatophilum: primitive low-potential cytochrome c. Proc Nat Acad Sci USA (1977) 74:5244-5247.

Kotelchuck D, Scheraga HA. The influence of short-range interactions on protein conformation. II. A model for predicting the alpha-helical regions of proteins. Proc Nat Acad Sci USA (1969) 62:14-21.

Kretsinger RH. Gene triplication deduced from the tertiary structure of a muscle calcium binding protein. Nature (1972) 240:85-88.

Kretsinger RH. Calcium-binding proteins. Annual Review of Biochemistry (1976) 45:239-266.

Kretsinger, RH. Structure and evolution of calcium-modulated proteins. CRC Crit Rev Biochem (1980) 8: 119-174.

Kretsinger RH, Nockolds CE. Carp muscle calcium-binding protein. II. Structure determination and general description. J Biol Chem (1973) 248:3313-3326.

Krimm S, Abe Y. Intermolecular interaction effects in the amide I vibrations of polypeptides. Proc Nat Acad Sci USA (1972) 69:2788-2792.

Kuntz ID. Protein folding. J Am Chem Soc (1972) 94:4009-4012.

Kuntz ID, Crippen GM, Kollmann PA, Kimelman D. Calculation of protein tertiary structure. J Mol Biol (1976) 106:983-994.

Kuntz ID, Kaufmann W. Hydration of Proteins & Polypeptides. Adv Prot Chem (1974) 28:239-345.

Ladenstein R, Epp O, Bartels K, Jones A, Huber R, Wendel A. Structure analysis and molecular model of the selenoenzyme glutathione peroxidase at 2.8 A resolution. J Mol Biol (1979) 134:199-218.

Ladner RC, Heidner EJ, Perutz MF. The structure of horse methaemoglobin at 2-0 Å resolution. J Mol Biol (1977) 114:385-414.

Lee BK, Richards FM. The Interpretation of Protein Structures: Estimation of Static Accessibility. J Mol Biol (1971) 55:379-400.

Leijonmarck M, Pettersson I, Liljas A. Structural aspects of recognition and assembly in biological macromolecules. In: Balaban M, editor; (1980) Weizmann Institute of Science, Rehovot, and Kibbutz Nof Ginossar, Israel. Balaban International Science Services: Glenside, PA.

Lesk AM, Chothia C. How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins. J Mol Biol (1980) 136:225-270.

Levine M, Muirhead H, Stammers DK, Stuart DI. Structure of pyruvate kinase and similarities with other enzymes: possible implications for protein taxonomy and evolution. Nature (1978) 271:626-630.

Levinthal C. Molecular model-building by computer. Sci Am (1966) 214:42-52.

Levinthal C. Are there pathways for protein folding? J Chem Phys (1968) 65:44-45.

Levitt M. Conformational preferences of amino acids in globular proteins. Biochemistry (1978) 17:4277-4285.

Levitt M, Chothia C. Structural patterns in globular proteins. Nature (1976) 261:552-558.

Levitt M, Greer J. Automatic identification of secondary structure in globular proteins. J Mol Biol (1977) 114:181-239.

Lewis PN, Go N, Go M, Kotelchuck D, Scheraga HA. Helix probability profiles of denatured proteins and their correlation with native structures. Proc Nat Acad Sci USA (1970) 65:810-815.

Lewis PN, Momany FA, Scheraga HA. Folding of polypeptide chains in proteins: a proposed mechanism for folding. Proc Nat Acad Sci USA (1971) 68:2293-2297.

Lewis PN, Momany FA, Scheraga HA. Chain reversals in proteins. Biochimica et Biophysica Acta (1973) 303:211-229.

Lifson S, Sander C. Antiparallel and parallel beta-strands differ in amino acid residue preferences. Nature (1979) 282:109-111.

Lifson S, Sander C. Specific recognition in the tertiary structure of beta-sheets of proteins. J Mol Biol 1980a; 139:627-639.

Lifson S, Sander C. Composition, Cooperativity and Recognition in Proteins. In: Jaenicke R, editor. Protein Folding. Amsterdam & New York: Elsevier/North-Holland Biomedical Publishing; 1980b. 289-316.

Lim VI. Structural principles of the globular organization of protein chains. A stereochemical theory of globular protein secondary structure. J Mol Biol 1974a; 88:857-872.

Lim VI. Algorithms for prediction of alpha-helical and beta-structural regions in globular proteins. J Mol Biol 1974b; 88:873-894.

Lim VI. Polypeptide chain folding through a highly helical intermediate as a general principle of globular protein structure formation. FEBS Lett (1978) 89:10-14.

Lindskog S, Henderson LE, Kannan KK, Liljas A, Nyman PO, Strandberg B. Carbonic Anhydrase: Crystal Structure Investigations. In: Boyer PD, editor. The Enzymes. 3rd ed. Volume 5. New York: Academic Press; 1971. p 608-622.

Lovell SC, Davis IW, Arendall WB, de Bakker PIW, Word JM, Prisant MG, Richardson JS, Richardson DC. Structure Validation by Cα Geometry: φ,ψ and Cβ Deviation. Proteins: Structure, Function and Genetics (2003) 50:437-450.

Lovell SC, Word JM, Richardson JS, Richardson DC. The penultimate rotamer library. Proteins: Structure, Function, and Genetics (2000) 40:389-408.

Low BW, Preston HS, Sato A, Rosen LS, Searl JE, Rudko AD, Richardson JS. Three dimensional structure of erabutoxin b neurotoxic protein: inhibitor of acetylcholine receptor. Proc Nat Acad Sci USA (1976) 73:2991-2994.

Lyu PC, Wemmer DE, Zhou HX, Pinker RJ, Kallenbach NR. Capping Interactions in Isolated α-Helices: Position-Dependent Substitution Effects and Structure of a Serine-Capped Peptide Helix. Biochemistry (1993) 32:421-425.

Maigret B, Pullmann B, Perahia D. Molecular orbital calculations on the conformation of polypeptides and proteins. VII. Refined calculations on the alanyl residue. J Theoret Biol (1971) 31:269-285.

Mandel N, Mandel G, Trus BL, Rosenberg J, Carlson G, Dickerson RE. Tuna cytochrome c at 2.0 Å Resolution. J Biol Chem (1977) 252:4619-4635.

Marquart M, Deisenhofer J, Huber R, Palm W. Crystallographic refinement and atomic models of the intact immunoglobulin molecule Kol and its antigen-binding fragment at 3.0 Å and 1.0 Å resolution. J Mol Biol (1980) 141:369-391.

Marshall SA, Morgan CS, Mayo SL. Electrostatics significantly affect the stability of designed homeodomain variants.J Mol Biol (2002) 316:189-99.

Matheson RR, Jr. , Scheraga HA. A Method for Predicting Nucleation Sites for Protein Folding Based on Hydrophobic Contacts. Macromolecules (1978) 11:819-829.

Mathews FS, Bethge PH, Czerwinski EW. The structure of cytochrome b562 from Escherichia coli at 2.5 Å resolution. J Biol Chem (1979) 254:1699-1706.

Mathews FS, Levine M, Argos P. Three-dimensional Fourier synthesis of calf liver cytochrome b 5 at 2-8Å resolution. J Mol Biol (1972) 64:449-464.

Matthews BW. The γ Turn. Evidence for a new folded conformation in proteins. Macromolecules (1972) 5:818-819.

Matthews BW. Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochimica et Biophysica Acta (1975) 405:442-451.

Matthews BW, Fenna RE, Bolognesi MC, Schmid MF, Olson JM. Structure of a bacteriochlorophyll a-protein from the green photosynthetic bacterium Prosthecochloris aestuarii. J Mol Biol (1979) 131:259-285.

Matthews BW, Remington SJ. The three dimensional structure of the lysozyme from bacteriophage T4. Proc Nat Acad Sci USA (1974) 71:4178-4182.

Matthews DA, Alden RA, Bolin JT, Freer ST, Hamlin R, Xuong N, Kraut J, Poe M, Williams M, Hoogsteen K. Dihydrofolate reductase: x-ray structure of the binary complex with methotrexate. Science (1977) 197:452-455.

Matthews DA, Alden RA, Freer ST, Xuong N-H, Kraut J. Dihydrofolate reductase from Lactobacillus casei. Stereochemistry of NADPH binding. J Biol Chem (1979) 254:4144-4151.

Mavridis IM, Tulinsky A. The folding and quaternary structure of trimeric 2-keto-3-deoxy-6-phosphogluconic aldolase at 3.5-Å resolution. Biochem (1976) 15:4410-4417.

Maxfield FR, Scheraga HA. Status of empirical methods for the prediction of protein backbone topography. Biochem (1976) 15:5138-5153.

McCammon JA, Gelin BR, Karplus M. Dynamics of folded proteins. Nature (1977) 267:585-590.

McLachlan AD. Gene duplication in the evolution of the yeast hexokinase active site. Eur J Biochem 1979a; 100:181-187.

McLachlan AD. Gene duplications in the structural evolution of chymotrypsin. J Mol Biol 1979b; 128:49-79.

McLachlan AD. Three-fold structural pattern in the soybean trypsin inhibitor (Kunitz). J Mol Biol 1979c; 133:557-563.

McLachlan AD, Bloomer AC, Butler PJG. Structural repeats and evolution of tobacco mosaic virus coat protein and RNA. J Mol Biol (1980) 136:203-224.

McPherson A, Jurnak FA, Wang AHJ, Molineux I, Rich A. Structure at 2.3 Å resolution of the gene 5 product of bacteriophage fd: a DNA unwinding protein. J Mol Biol (1979) 134:379-400.

Mitsui Y, Satow Y, Watanabe Y, Iitaka Y. Crystal structure of a bacterial protein proteinase inhibitor (Streptomyces subtilisin inhibitor) at 2.6 Å resolution. J Mol Biol (1979) 131:697-724.

Miyazawa T, Blout ER. The Infrared Spectra of Polypeptides in Various Conformations: Amide I and II Bands. J Am Chem Soc (1961) 83:712-719.

Momany FA, McGuire RF, Burgess AW, Scheraga HA. Energy Parameters in Polypeptides. VII. Geometric Parameters, Partial Atomic Changes, Nonbonded Interactions, Hydrogen Bond Interactions, and Intrinsic Torsional Potentials for the Naturally Occurring Amino Acids. J Phys Chem (1975) 79:2361-2381.

Monaco HL, Crawford JL, Lipscomb WN. Three-dimensional structures of aspartate carbamoyltransferase from Escherichia coli and of its complex with cytidine triphosphate. Proc Nat Acad Sci USA (1978) 75:5276-5280.

Mornon JP, Fridlansky F, Bally R, Milgrom E. X-ray crystallographic analysis of a progesterone-binding protein. The C2221 crystal form of oxidized uteroglobin at 2.2 Å resolution. J Mol Biol (1980) 137:415-429.

Mowbray SL, Helgstrand C, Sigrell JA, Cameron AD, Jones TA. Errors and reproducibility in electron-density map interpretation. Acta Cryst. D (1999) 55:1309-1319.

Muñoz V, Blanco FJ, Serrano L. The hydrophobic-staple motif and a role for loop residues in α-helix stability and protein folding. Nat. Struct. Biol. (1995) 2:380-385.

Munñoz V, Serrano L. Elucidating the folding problem of helical peptides using empirical parameters. Nat. Struct. Biol. (1994)1: 399-409.

Murray LJW, Arendall WB, Richardson DC, Richardson JS. RNA Backbone is Rotameric. Proceedings of the National Academy of Sciences USA (2003) 100:13904-13909.

Murzin, AG and Finkelstein, AV. General architecture of the alpha-helical globule. J Mol Biol (1988) 204: 749-770.

Nagano K. Logical analysis of the mechanism of protein folding II. The nucleation process. J Mol Biol (1974) 84:337-372.

Nagano K. Logical analysis of the mechanism of protein folding. IV. Super-secondary structures. J Mol Biol 1977a; 109:235-250.

Nagano K. Triplet information in helix prediction applied to the analysis of super-secondary structures. J Mol Biol 1977b; 109:251-274.

Némethy G, Gibson KD, Palmer KA, Yoon CN, Paterlini G, Zagari A, Rumsey S, Scheraga HA. Energy Parameters in Polypeptides. 10. Improved Geometrical Parameters and Nonbonded Interactions for Use in the ECEPP/3 Algorithm, with Application to Proline-Containing Peptides. Journal of Physical Chemistry (1992) 96:6472-6484.

Némethy G, Phillips DC, Leach SJ, Scheraga HA. A second right-handed helical structure with the parameters of the Pauling-Corey alpha-helix. Nature (1967) 214:363-365.

Némethy G, Printz MP. The γ Turn, a possible folded conformation of the polypeptide chain. Comparison with the β turn. Macromolecules (1972) 5:755-758.

Nicholson H, Anderson DE, Dao-pin S, Matthews B. Analysis of the Interaction between Charged Side Chains and α-Helix Dipole Using Designed Thermostable Mutants of Phage T4 Lysozyme Biochemistry(1991) 30: 9816-9828.

Nomenclature I-ICoB. Abbreviations and Symbols for the Description of the Conformation of Polypeptide Chains. Tentative Rules. J Biol Chem (1970) 245:6489 - 6497.

O`Shea, EK, Klemm, JD, Kim, PS, Alber, T. X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. Science (1991) 254: 539-544.

Oughton BM, Harrison PM. The crystal structure of hexagonal L-cystine. Acta Cryst (1957) 10:479-480.

Oughton BM, Harrison PM. The crystal structure of hexagonal L-cystine. Acta Cryst (1959) 12:396-404.

Pain RH, Robson B. Analysis of the code relating sequence to secondary structure in proteins. Nature (1970) 227:62-63.

Pauling L, Corey RB, Branson HR. The Structure of Proteins: Two Hydrogen-Bonded Helical Configurations of the Polypeptide Chain. Proc Nat Acad Sci USA 1951a; 37:205-211.

Pauling L, Corey RB. Configurations of Polypeptide Chains with Favored Orientations Around Single Bonds: Two New Pleated Sheets. Proc Nat Acad Sci USA 1951b; 37:729-740.

Perutz MF. An X-Ray Study of Horse Methaemoglobin. II. Proceedings of the Royal Society of London Series A (1949) 195:474-499.

Perutz MF. New X-ray evidence on the configuration of polypeptide chains. Nature (1951) 167:1053-1054.

Perutz MF. The Hemoglobin Molecule. Sci Am (1964) 211:64-76.

Perutz MF. Stereochemistry of cooperative effects in haemoglobin. Nature (1970) 228:726-739.

Perutz MF. Hemoglobin structure and respiratory transport. Sci Am (1978) 239:92-125.

Peterson J, Steinrauf LK, Jensen LH. Direct determination of the structure of L-cystine dihydrobromide. Acta Cryst (1960) 13:104-109.

Pickover CA, McKay DB, Engelman DM, Steitz TA. Substrate binding closes the cleft between the domains of yeast phosphoglycerate kinase. J Biol Chem (1979) 254:11323-11329.

Ploegman JH, Drent G, Kalk KH, Hol WGJ. Structure of bovine liver rhodanese. I. Structure determination at 2.5 A resolution and a comparison of the conformation and sequence of its two domains. J Mol Biol (1978) 123:557-594.

Ponder JW, Richards FM. Tertiary Templates for Proteins: Use of Packing Criteria in the Enumeration of Allowed Sequences for Different Structural Classes. JMB (1987) 193:775-791.

Poulos TL, Freer ST, Alden RA, Edwards SL, Skogland U, Takio K, Eriksson B, Xuong N-H, Yonetani T, Kraut J. The crystal structure of cytochrome c peroxidase. J Biol Chem (1980) 255:575-580.

Prothero JW. Correlation between the distribution of amino acids and alpha helices. Biophys J (1966) 6:367-370.

Ptitsyn OB. Statistical analysis of the distribution of amino acid residues among helical and non-helical regions in globular proteins. J Mol Biol (1969) 42:501-510.

Ptitsyn OB, Finkelstein AV. Self-organization of proteins and the problem of their three-dimensional structure prediction. In: Jaenicke R, editor. Protein Folding. Amsterdam & New York: Elsevier/North-Holland Biomedical Press; 1980. p 101-115.

Ptitsyn OB, Rashin AA. A model of myoglobin self-organization. Biophys Chem (1975) 3:1-20.

Pullman B, Pullman A. Molecular orbital calculations on the conformation of amino acid residues of proteins. Adv Prot Chem (1974) 28:347-526.

Quiocho FA, Gilliland GL, Phillips GN, Jr. The 2.8-Å resolution structure of the L-arabinose-binding protein from Escherichia coli. Polypeptide chain folding, domain similarity, and probable location of sugar-binding site. J Biol Chem (1977) 252:5142-5149.

Quiocho FA, Lipscomb WN. Carboxypeptidase A: a protein and an enzyme. Adv Prot Chem (1971) 25:1-78.

Raghavendra K, Sasisekharan V. Conformational analysis of the right-hand twisted antiparallel beta-structure. International Journal of Peptide & Protein Research (1979) 14:326-338.

Ralston E, DeCoen JL. Folding of polypeptide chains induced by the amino acid side-chains. J Mol Biol (1974) 83:393-420.

Ramachandran GN. Part I. Conformational Calculations: Aspects of Peptide Conformation. In: Blout ER, Bovey FA, Goodman M, Lotan N, editors. Peptides, Polypeptides, & Proteins. New York: Wiley-Interscience; 1974. p 14-34.

Ramachandran GN, Ramakrishnan C, Sasisekharan V. Stereochemistry of Polypeptide Chain Configurations. J Mol Biol (1963) 7:95-99.

Ramachandran GN, Sasisekharan V. Conformation of polypeptides and proteins. Adv Prot Chem (1968) 23:284-438.

Rao ST, Rossmann MG. Comparison of super-secondary structures in proteins. J Mol Biol (1973) 76:241-256.

Reeke GN, Jr., Becker JW, Edelman GM. The covalent and three-dimensional structure of concanavalin A. IV. Atomic coordinates, hydrogen bonding, and quaternary structure. J Biol Chem (1975) 250:1525-1547.

Remington SJ, Matthews BW. A general method to assess similarity of protein structures, with applications to T4 bacteriophage lysozyme. Proc Nat Acad Sci USA (1978) 75:2180-2184.

Remington SJ, Matthews BW. A systematic approach to the comparison of protein structures. J Mol Biol (1980) 140:77-99.

Richards FM. Area, volumes, packing, and protein structure. Ann Rev Biophys Bioeng (1977) 6:151-176.

Richardson DC, Richardson JS. Principles and Patterns of Protein Conformation. In Prediction of Protein Structure and the Principles of Protein Conformation, G.D. Fasman, Ed., 1 ed. New York: Plenum Press (1989)1-98.

Richardson JS. Handedness of Crossover Connections in Beta Sheets. Proc Nat Acad Sci USA (1976) 73:2619-2623.

Richardson JS. Beta-sheet topology and the relatedness of proteins. Nature (1977) 268:495-500.

Richardson JS. The Singly-wound Parallel Beta-Barrel: A Proposed Structure for 2-keto-deoxy-6-phosphogluconate aldolase. Biochem Biophys Res Comm (1979) 90:285-290.

Richardson JS. The Anatomy and Taxonomy of Protein Structure. Advances in Protein Chemistry (1981) 34:167-339.

Richardson JS, Getzoff ED, Richardson DC. The Beta Bulge: A Common Small Unit of Non-Repetitive Protein Structure. Proc Nat Acad Sci USA (1978) 75:2574-2578.

Richardson, JS and Richardson, DC. Amino-acid preferences for specific locations at the end of alpha-helices. Science (1988) 240: 1648-1652.

Richardson JS, Richardson DC, Thomas KA, Silverton EW, Davies DR. Similarity of Three-Dimensional Structure Between the Immunoglobulin Domain and the Cu,Zn Superoxide Dismutase Subunit. J Mol Biol (1976) 102:221-235.

Richardson JS, Thomas KA, Rubin BH, Richardson DC. Crystal Structure of Bovine Cu,Zn Superoxide Dismutase at 3Å Resolution: Chain Tracing and Metal Ligands. Proc Nat Acad Sci USA (1975) 72:1349-1353.

Richmond TJ, Richards FM. Packing of alpha-helices: geometrical constraints and contact areas. J Mol Biol (1978) 119:537-555.

Rose GD. Prediction of chain turns in globular proteins on a hydrophobic basis. Nature (1978) 272:586-590.

Rose GD. Hierarchic organization of domains in globular proteins. J Mol Biol (1979) 134:447-470.

Rose GD, Seltzer JP. A new algorithm for finding the peptide chain turns in a globular protein. J Mol Biol (1977) 113:153-164.

Rose GD, Winters RH, Wetlaufer DB. A testable model for protein folding. FEBS Lett (1976) 63:10-16.

Rossmann MG, Argos P. Exploring structural homology of proteins. J Mol Biol (1976) 105:75-95.

Rossmann MG, Moras D, Olsen KW. Chemical and biological evolution of nucleotide-binding protein. Nature (1974) 250:194-199.

Rost, B and Sander, C. Third generation prediction of protein secondary structure. Methods Mol Biol (2000) 143: 71-95.

Sakano H, Rogers JH, Hüppi K, Brack C, Traunecker A, Maki R, Wall R, Tonegawa S. Domains and the hinge region of an immunoglobulin heavy chain are encoded in separate DNA segments. Nature (1979) 277:627-633.

Salemme FR. Structural properties of protein beta-sheets. Progress in Biophysics & Molecular Biology (1983) 42:95-133.

Salemme FR, Freer ST, Xuong N-H, Alden RA, Kraut J. The structure of oxidized cytochrome c 2 of Rhodospirillum rubrum. J Biol Chem (1973) 248:3910-3921.

Saul FA, Amzel LM, Poljak RJ. Preliminary refinement and structural analysis of the Fab fragment from human immunoglobulin new at 2.0 Å resolution. J Biol Chem (1978) 253:585-597.

Sawyer L, Shotton DM, Campbell JW, Wendell PL, Muirhead H, Watson HC, Diamond R, Ladner RC. The atomic structure of crystalline porcine pancreatic elastase at 2.5 Å resolution: comparisons with the structure of alpha-chymotrypsin. J Mol Biol (1978) 118:137-208.

Saxena VP, Wetlaufer DB. A new basis for interpreting the circular dichroic spectra of proteins. Proc Nat Acad Sci USA (1971) 68:969-972.

Schellman CG. The alpha-L conformation at the ends of helices. In: Jaenicke R, editor. Protein Folding. Amsterdam: Elsevier/North-Holland Biomedical Press; 1980. p 53-61.

Schiffer M, Edmundson AB. Use of helical wheels to represent the structures of proteins and to identify segments with helical potential. Biophys J (1967) 7:121-135.

Schiffer M, Girling RL, Ely KR, Edmundson AB. Structure of a lambda-type Bence-Jones protein at 3.5-Å resolution. Biochem (1973) 12:4620-4631.

Schulz GE. Gene duplication in glutathione reductase. J Mol Biol (1980) 138:335-347.

Schulz GE, Barry CD, Friedman J, Chou PY, Fasman GD, Finkelstein AV, Lim VI, Ptitsyn OB, Kabat EA, Wu TT, Levitt M, Robson B, Nagano K. Comparison of predicted and experimentally determined secondary structure of adenyl kinase. Nature 1974b; 250:140-142.

Schulz GE, Elzinga M, Marx F, Schirmer RH. Three dimensional structure of adenyl kinase. Nature 1974a; 250:120-123.

Schulz GE, Schirmer RH. Topological comparison of adenyl kinase with other proteins. Nature 1974c; 250:142-144.

Schulz GE, Schirmer RH, Sachsenheimer W, Pai EF. The structure of the flavoenzyme glutathione reductase. Nature (1978) 273:120-124.

Serrano L, Fersht AR. Capping and α-helix stability. Nature (1989) 342:296-299.

Shaw PJ, Muirhead H. Crystallographic structure analysis of glucose 6-phosphate isomerase at 3-5 Å resolution. J Mol Biol (1977) 109:475-485.

Sheridan RP, Lee RH, Peters N, Allen LC. Hydrogen-Bond Cooperativity in Protein Secondary Structure. Biopolymers (1979) 18:2451-2458.

Sibanda BL, Thornton JM. β-Hairpin families in globular proteins. Nature (1985) 316:170-174.

Silverton EW, Navia MA, Davies DR. Three-dimensional structure of an intact human immunoglobulin. Proc Nat Acad Sci USA (1977) 74:5140-5144.

Spiro TG, Gaber BP. Laser Raman scattering as a probe of protein structure. Annual Review of Biochemistry (1977) 46:553-572.

Sprang S, Fletterick RJ. The structure of glycogen phosphorylase alpha at 2.5 Å resolution. J Mol Biol (1979) 131:523-551.

Srinivasan R, Balasubramanian R, Rajan SS. Extended helical conformation newly observed in protein folding. Science (1976) 194:720-722.

Staphylococcus-Aureus. Hoppe-Seylers Z Physiol Chem 1978;359: 975-985.

Steinrauf LK, Peterson J, Jensen LH. The Crystal Structure of L-Cystine Hydrochloride. J Am Chem Soc (1958) 80:3835-3838.

Steitz TA, Fletterick RJ, Anderson WF, Anderson CM. High resolution x-ray structure of yeast hexokinase, an allosteric protein exhibiting a non-symmetric arrangement of subunits. J Mol Biol (1976) 104:197-222.

Steitz, TA, Ohlendorf, DH, McKay, DB, Anderson, WF, Matthews, BW. Structural similarity in the DNA-binding domains of catabolite gene activator and cro repressor proteins. Proc Nat Acad Sci (1982) 79: 3097-3100.

Stenkamp RE, Sieker LC, Jensen LH, McQueen JE, Jr. Structure of methemerythrin at 2.8-Angstrom resolution: computer graphics fit of an averaged electron density map. Biochem (1978) 17:2499-2504.

Sternberg MJE, Thornton JM. On the conformation of proteins: the handedness of the beta-strand-alpha-helix-beta-strand unit. J Mol Biol (1976) 105:367-382.

Sternberg MJE, Thornton JM. On the conformation of proteins: the handedness of the connection between parallel beta-strands. J Mol Biol 1977a; 110:269-283.

Sternberg MJE, Thornton JM. On the conformation of proteins: an analysis of beta-pleated sheets. J Mol Biol 1977b; 110:285-296.

Sternberg MJE, Thornton JM. On the conformation of proteins: hydrophobic ordering of strands in beta-pleated sheets. J Mol Biol 1977c; 115:1-17.

Stroud RM, Kay LM, Dickerson RE. The structure of bovine trypsin: electron density maps of the inhibited enzyme at 5 Angstrom and at 2-7 Angstrom resolution. J Mol Biol (1974) 83:185-208.

Stuart DI, Levine M, Muirhead H, Stammers DK. Crystal structure of cat muscle pyruvate kinase at a resolution of 2.6 A. J Mol Biol (1979) 134:109-142.

Subramanian E, Swan IDA, Liu M, Davies DR, Jenkins JA, Tickle IJ, Blundell TL. Homology among acid proteases: comparison of crystal structures at 3A resolution of acid proteases from Rhizopus chinensis and Endothia parasitica. Proc Nat Acad Sci USA (1977) 74:556-559.

Sugeta H, Go A, Miyazawa T. S-S and C-S stretching vibrations and molecular conformations of dialkyl disulfides and cystine. Chem Lett (1972) 83-86.

Sugeta H, Go A, Miyazawa T. Vibrational spectra and molecular conformations of dialkyl disulfides. Bull Chem Soc Jpn (1973) 46:3407-3411.

Swanson R, Trus BL, Mandel N, Mandel G, Kallai OB, Dickerson RE. Tuna cytochrome c at 2.0 Å resolution. I.Ferricytochrome structure analysis. J Biol Chem 1977a; 252:759-775.

Sweet RM, Wright HT, Janin J, Chothia C, Blow DM. Crystal structure of the complex of porcine trypsin with soybean trypsin inhibitor (Kunitz) at 2.6-A resolution. Biochem (1974) 13:4212-4228.

Sygusch J, Madsen NB, Kasvinsky PJ, Fletterick RJ. Location of pyridoxal phosphate in glycogen phosphorylase a. Proc Nat Acad Sci USA (1977) 74:4757-4761.

Tanaka S, Scheraga HA. Model of Protein Folding: Inclusion of Short-, Medium-, and Long-Range Interactions. Proc Nat Acad Sci USA (1977) 72:3802-3806.

Taniuchi H, Anfinsen CB. An experimental approach to the study of the folding of staphylococcal nuclease. J Biol Chem (1969) 244:3864-3875.

Timkovich R, Dickerson RE. Recurrence of the cytochrome fold in a nitrate-respiring bacterium. J Mol Biol (1973) 79:39-56.

Tramontano A, Morea V. Assessment of homology-based predictions in CASP5.. Proteins (2003) 53 (Suppl 6):352-368.

Tsernoglou D, Petsko GA. Three-dimensional structure of neurotoxin a from venom of the Philippines sea snake. Proc Nat Acad Sci USA (1977) 74:971-974.

Tulinsky A, Vandlen RL, Morimoto CN, Mani NV, Wright LH. Variability in the tertiary structure of alpha-chymotrypsin at 2.8-Å resolution. Biochem (1973) 12:4185-4192.

Vainshtein BK, Melik-Adamyan VR, Barynin VV, Vagin AA. X-ray diffraction investigation of catalase of Penicillium vitale with 3.5Å reslution. Dokl Akad Nauk SSSR (1980) 250:242-246 (English translation pp. 249-213).

Van Wart HE, Lewis A, Scheraga HA, Saeva FD. Disulfide Bond Dihedral Angles from Raman Spectroscopy. Proc Nat Acad Sci USA (1973) 70:2619-2623.

Van Wart HE, Scheraga HA. Raman spectra of strained disulfides. Effect of rotation about sulfur-sulfur bonds on sulfur-sulfur stretching frequencies. J Phys Chem (1976) 80:1823-1832.

Venkatachalam CM. Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units. Biopolymers (1968) 6:1425-1436.

Vojtechovsky J, Chu K, Berendzen J, Sweet RM, Schlichting I. Crystal Structures of Myoglobin-Ligand Complexes at Near-Atomic Resolution. Biophys.J. (1999) 77:2153-2164.

Wagner G, Wüthrich K. Dynamic model of globular protein conformations based on NMR studies in solution. Nature (1978) 275:247-248.

Walkinshaw MD, Saenger W, Maelicke A. Three-dimensional structure of the "long" neurotoxin from cobra venom. Proc Nat Acad Sci USA (1980) 77:2400-2404.

Wang B-C, Yoo CS, Sax M. Crystal structure of Bence Jones protein rhe (3 A) and its unique domain-domain association. J Mol Biol (1979) 129:657-674.

Ward KB, Hendrickson WA, Klippenstein GL. Quaternary and tertiary structure of haemerythrin. Nature (1975) 257:818-821.

Warme PK, Morgan RS. A survey of amino acid side-chain interactions in 21 proteins. J Mol Biol 1978b; 118:289-304.

Watenpaugh KD, Margulis TN, Sieker LC, Jensen LH. Water structure in a protein crystal: rubredoxin at 1.2 Å resolution. J Mol Biol (1978) 122:175-190.

Watenpaugh KD, Sieker LC, Jensen LH. Crystallographic refinement of rubredoxin at 1 x 2 Å degrees resolution. J Mol Biol (1980) 138:615-633.

Watenpaugh KD, Sieker LC, Jensen LH. The structure of rubredoxin at 1.2 Å resolution. J Mol Biol (1979) 131:509-522.

Watson HC. Stereochemistry of the protein myoglobin. Prog Stereochem (1969) 4:229-333.

Weatherford DW, Salemme FR. Conformations of twisted parallel beta-sheets and the origin of chirality in protein structures. Proc Nat Acad Sci USA (1979) 76:19-23.

Weber IT, Johnson LN, Wilson KS, Yeates DGR, Wild DL, Jenkins JA. Crystallographic studies on the activity of glycogen phosphorylase b. Nature (1978) 274:433-437.

Weber PC, Bartsch RG, Cusanovich MA, Hamlin RC, Howard A, Jordan SR, Kamen MD, Meyer TE, Weatherford DW, Xuong N-H, Salemme FR. Structure of cytochrome c': a dimeric, high-spin haem protein. Nature (1980) 286:302-304.

Wetlaufer DB. Nucleation, rapid folding, and globular intrachain regions in proteins. Proc Nat Acad Sci USA (1973) 70:697-701.

Wiegand G, Kukla D, Scholze H, Jones TA, Huber R. Crystal structure analysis of the tetragonal crystal form are preliminary molecular model of pig-heart citrate synthase. Eur J Biochem (1979) 93:41-50.

Wierenga RK, de Jong RJ, Kalk KH, Hol WGJ, Drenth J. Crystal structure of p-hydroxybenzoate hydroxylase. J Mol Biol (1979) 131:55-73.

Wilson IA, Skehel JJ, Wiley DC. Structure of the haemagglutinin membrane glycoprotein of influenza virus at 3 Å resolution. Nature (1981) 289:366-373.

Wodak SJ, Janin J. Analytical Approximation to the Accessible Surface Area of Proteins. Proc Nat Acad Sci USA (1980) 77:1736-1740.

Wolfenden R. Interaction of the peptide bond with solvent water: a vapor phase analysis. Biochem (1978) 17:201-204.

Wright CS. The crystal structure of wheat germ agglutinin at 2-2 Å resolution. J Mol Biol (1977) 111:439-457.

Wright CS, Alden RA, Kraut J. Structure of subtilisin BPN' at 2.5 angstrom resolution. Nature (1969) 221:235-242.

Wright HT. Comparison of the crystal structures of chymotrypsinogen-A and alpha-chymotrypsin. J Mol Biol 1973a; 79:1-11.

Wright HT. Activation of chymotrypsinogen-A. An hypothesis based upon comparison of the crystal structures of chymotrypsinogen-A and alpha-chymotrypsin. J Mol Biol 1973b; 79:13-23.

Wrinch DM. The cyclol hypothesis and the "globular" proteins. Proc R Soc London Ser A (1937) 161:505-524.

Wu TT, Szu SC, Jernigan RL, Bilofsky H, Kabat EA. Prediction of beta-sheets in immunoglobulin-chains - Comparison of various methods and an expanded 20X20 table for evaluation of effects of nearest-neighbors on conformations of middle amino-acids in proteins. Biopolymers (1978) 17:555-572.

Wyckoff HW, Tsernoglou D, Hanson AW, Knox JR, Lee B, Richards FM. The three-dimensional structure of ribonuclease-S. Interpretation of an electron density map at a nominal resolution of 2 Å. J Biol Chem (1970) 245:305-328.

Yakel HL, Jr., Hughes EW. The crystal structure of N,N'-diglycyl-L-cystine dihydrate. Acta Cryst (1954) 7:291-297.

Yaron A, Katchalski E, Berger A, Fasman GD, Sober HA. The chain length dependence of the conformation for oligomers of L-lysine in aqueous solution: optical rotatory dispersion studies. Biopolymers (1971) 10:1107-1120.

Yu N-T, Lin T-S, Tu AT. Laser Raman scattering of neurotoxins isolated from the venoms of sea snakes Lapemis hardwickii and Enhydrina schistosa. J Biol Chem (1975) 250:1782-1785.

Zimmerman SS, Scheraga HA. Influence of local interactions on protein structure. I. Conformational energy studies of N-acetyl-N'-methylamides of Pro-X and X-Pro dipeptides. Biopolymers 1977a; 16:811-843.

Zimmerman SS, Scheraga HA. Local interactions in bends of proteins. Proc Nat Acad Sci USA 1977b; 74:4126-4129.