Integrating protein structural information
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[1] K. S. Arun,et al. Least-Squares Fitting of Two 3-D Point Sets , 1987, IEEE Transactions on Pattern Analysis and Machine Intelligence.
[2] Rolf Backofen. The Protein Structure Prediction Problem: A Constraint Optimization Approach using a New Lower Bound , 2004, Constraints.
[3] Martin Zacharias,et al. Protein–protein docking with a reduced protein model accounting for side‐chain flexibility , 2003, Protein science : a publication of the Protein Society.
[4] Rolf Backofen. Constraint Techniques for Solving the Protein Structure Prediction Problem , 1998, CP.
[5] Richard A. Volz,et al. Estimating 3-D location parameters using dual number quaternions , 1991, CVGIP Image Underst..
[6] Ludwig Krippahl,et al. Modeling protein complexes with BiGGER , 2003, Proteins.
[7] P. Kollman,et al. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .
[8] R. G. Hart,et al. Structure of Myoglobin: A Three-Dimensional Fourier Synthesis at 2 Å. Resolution , 1960, Nature.
[9] Pedro Barahona,et al. PSICO: Solving Protein Structures with Constraint Programming and Optimization , 2002, Constraints.
[10] M. Jaskólski,et al. Conserved folding in retroviral proteases: crystal structure of a synthetic HIV-1 protease. , 1989, Science.
[11] Hongmin Li,et al. Structures of two streptococcal superantigens bound to TCR beta chains reveal diversity in the architecture of T cell signaling complexes. , 2002, Structure.
[12] S. B. Needleman,et al. A general method applicable to the search for similarities in the amino acid sequence of two proteins. , 1970, Journal of molecular biology.
[13] E. Purcell,et al. Relaxation Effects in Nuclear Magnetic Resonance Absorption , 1948 .
[14] C. Gille,et al. Conservation of substructures in proteins: interfaces of secondary structural elements in proteasomal subunits. , 2000, Journal of molecular biology.
[15] D. Ritchie,et al. Protein docking using spherical polar Fourier correlations , 2000, Proteins.
[16] M Czjzek,et al. Heteronuclear NMR and soft docking: an experimental approach for a structural model of the cytochrome c553-ferredoxin complex. , 2000, Biochemistry.
[17] A J Olson,et al. Structural symmetry and protein function. , 2000, Annual review of biophysics and biomolecular structure.
[18] Yehezkel Lamdan,et al. On recognition of 3-D objects from 2-D images , 2011, Proceedings. 1988 IEEE International Conference on Robotics and Automation.
[19] Barry Honig,et al. Focusing of electric fields in the active site of Cu‐Zn superoxide dismutase: Effects of ionic strength and amino‐acid modification , 1986, Proteins.
[20] Joxan Jaffar,et al. Constraint logic programming , 1987, POPL '87.
[21] G. Zanetti,et al. Structural studies on the interaction between ferredoxin and ferredoxin-NADP+ reductase , 1988 .
[22] R. Huber,et al. Crystal structure of desulforedoxin from Desulfovibrio gigas determined at 1.8 A resolution: a novel non-heme iron protein structure. , 1995, Journal of molecular biology.
[23] L. Pauling,et al. Atomic coordinates and structure factors for two helical configurations of polypeptide chains. , 1951, Proceedings of the National Academy of Sciences of the United States of America.
[24] Françoise Guerlesquin,et al. A novel approach for assesing macromolecular complexes combining soft‐docking calculations with NMR data , 2001, Protein science : a publication of the Protein Society.
[25] Robert B. Fisher,et al. Estimating 3-D rigid body transformations: a comparison of four major algorithms , 1997, Machine Vision and Applications.
[26] J. Kuriyan,et al. High resolution crystal structure of a paired (Pax) class cooperative homeodomain dimer on DNA , 1995, Cell.
[27] Wei Zu Chen,et al. A soft docking algorithm for predicting the structure of antibody‐antigen complexes , 2003, Proteins.
[28] D. Nurizzo,et al. MAD structure of Pseudomonas nautica dimeric cytochrome c552 mimicks the c4 Dihemic cytochrome domain association. , 1999, Journal of molecular biology.
[29] M. Sternberg,et al. Modelling protein docking using shape complementarity, electrostatics and biochemical information. , 1997, Journal of molecular biology.
[30] Teuvo Kohonen,et al. Self-organized formation of topologically correct feature maps , 2004, Biological Cybernetics.
[31] Joël Janin,et al. Welcome to CAPRI: A Critical Assessment of PRedicted Interactions , 2002 .
[32] J. V. Van Beeumen,et al. Evidence for a ternary complex formed between flavodoxin and cytochrome c3: 1H-NMR and molecular modeling studies. , 1994, Biochemistry.
[33] E. Aronson,et al. Theory and method , 1985 .
[34] R. Hille,et al. Electron transfer in milk xanthine oxidase as studied by pulse radiolysis. , 1991, The Journal of biological chemistry.
[35] A. Fersht,et al. Protein-protein recognition: crystal structural analysis of a barnase-barstar complex at 2.0-A resolution. , 1994, Biochemistry.
[36] John J. Hopfield,et al. Electron tunneling through covalent and noncovalent pathways in proteins , 1987 .
[37] M. Carter. Computer graphics: Principles and practice , 1997 .
[38] J. Onuchic,et al. A NEW FRAMEWORK FOR ELECTRON-TRANSFER CALCULATIONS-BEYOND THE PATHWAYS-LIKE MODELS , 1998 .
[39] C. Enroth,et al. Crystal structures of bovine milk xanthine dehydrogenase and xanthine oxidase: structure-based mechanism of conversion. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[40] Ludwig Krippahl,et al. Electron transfer complexes of cytochrome c peroxidase from Paracoccus denitrificans containing more than one cytochrome. , 2003, Biochemistry.
[41] R. A. Scott,et al. Discriminating compact nonnative structures from the native structure of globular proteins. , 1995, Proceedings of the National Academy of Sciences of the United States of America.
[42] Pascal Van Hentenryck,et al. A Generic Arc-Consistency Algorithm and its Specializations , 1992, Artif. Intell..
[43] M. Bruschi,et al. The nucleotide sequence of the Desulfovibrio gigas desulforedoxin gene indicates that the Desulfovibrio vulgaris rbo gene originated from a gene fusion event , 1990, Journal of bacteriology.
[44] L. Sieker,et al. Structure of the oxidized form of a flavodoxin at 2.5-Angstrom resolution: resolution of the phase ambiguity by anomalous scattering. , 1972, Proceedings of the National Academy of Sciences of the United States of America.
[45] Alan K. Mackworth. Consistency in Networks of Relations , 1977, Artif. Intell..
[46] Rolf Backofen,et al. Protein similarity search under mRNA structural constraints: application to selenocysteine incorporation , 2002, Silico Biol..
[47] Haim J. Wolfson,et al. Geometric hashing: an overview , 1997 .
[48] R. Hille. The Mononuclear Molybdenum Enzymes. , 1997, Chemical reviews.
[49] B. Tidor. Molecular dynamics simulations , 1997, Current Biology.
[50] L. Pauling,et al. The pleated sheet, a new layer configuration of polypeptide chains. , 1951, Proceedings of the National Academy of Sciences of the United States of America.
[51] D. Goodsell,et al. Automated docking of substrates to proteins by simulated annealing , 1990, Proteins.
[52] Eric J. Sorin,et al. Beta-hairpin folding simulations in atomistic detail using an implicit solvent model. , 2001, Journal of molecular biology.
[53] P. Sellers. On the Theory and Computation of Evolutionary Distances , 1974 .
[54] Roman Barták,et al. Constraint Programming - What is behind? , 1999 .
[55] Preliminary crystallographic analysis of the oxidized form of a two mono‐nuclear iron centres protein from desulfovibrio desulfuricans ATCC 27774 , 1996, Protein science : a publication of the Protein Society.
[56] A. Rosato,et al. A further investigation of the cytochrome b5–cytochrome c complex , 2003, JBIC Journal of Biological Inorganic Chemistry.
[57] Toby Walsh,et al. An Empirical Study of Dynamic Variable Ordering Heuristics for the Constraint Satisfaction Problem , 1996, CP.
[58] C. Dominguez,et al. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. , 2003, Journal of the American Chemical Society.
[59] Eleanor J. Gardiner,et al. Protein docking using a genetic algorithm , 2001, Proteins.
[60] Simon Haykin,et al. Neural Networks: A Comprehensive Foundation , 1998 .
[61] Dudley H. Williams,et al. Partitioning of free energy contributions in the estimation of binding constants : Residual motions and consequences for amide-amide hydrogen bond strengths , 1992 .
[62] J. Richardson,et al. The penultimate rotamer library , 2000, Proteins.
[63] J. Thornton,et al. Atlas of protein side-chain interactions , 1992 .
[64] John Harris,et al. Handbook of mathematics and computational science , 1998 .
[65] J. Nocedal,et al. A Limited Memory Algorithm for Bound Constrained Optimization , 1995, SIAM J. Sci. Comput..
[66] Martin T. Swain,et al. Modelling Protein Side-chain Conformations using Constraint Logic Programming , 2002, Comput. Chem..
[67] Ivan E. Sutherland,et al. Sketchpad: a man-machine graphical communication system , 1899, AFIPS '63 (Spring).
[68] Pierre Baldi,et al. Bioinformatics - the machine learning approach (2. ed.) , 2000 .
[69] W. Torgerson. Multidimensional scaling: I. Theory and method , 1952 .
[70] L. Krippahl,et al. BiGGER: A new (soft) docking algorithm for predicting protein interactions , 2000, Proteins.
[71] Magali Mathieu,et al. Atomic structure of the major capsid protein of rotavirus: implications for the architecture of the virion , 2001, The EMBO journal.
[72] M. Perutz,et al. Three dimensional fourier synthesis of horse deoxyhaemoglobin at 2.8 Angstrom units resolution. , 1970, Nature.
[73] David S. Goodsell,et al. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function , 1998, J. Comput. Chem..
[74] Stephen E Harding,et al. The electron transfer complexes of cytochrome c peroxidase from Paracoccus denitrificans. , 2003, Biochemistry.
[75] Kirill Degtyarenko,et al. PROMISE: a database of bioinorganic motifs , 1999, Nucleic Acids Res..
[76] G T Montelione,et al. Automated sequencing of amino acid spin systems in proteins using multidimensional HCC(CO)NH-TOCSY spectroscopy and constraint propagation methods from artificial intelligence , 1994, Journal of biomolecular NMR.
[77] Zhiping Weng,et al. A protein–protein docking benchmark , 2003, Proteins.
[78] J. V. Van Beeumen,et al. The surface-charge asymmetry and dimerisation of cytochrome c550 from Paracoccus denitrificans--implications for the interaction with cytochrome c peroxidase. , 1998, European journal of biochemistry.
[79] Berthold K. P. Horn,et al. Closed-form solution of absolute orientation using orthonormal matrices , 1988 .
[80] R Nussinov,et al. Efficient computational algorithms for docking and for generating and matching a library of functional epitopes I. Rigid and flexible hinge-bending docking algorithms. , 1999, Combinatorial chemistry & high throughput screening.
[81] T. Yamazaki,et al. Structure of the electron transfer complex between ferredoxin and ferredoxin-NADP+ reductase , 2001, Nature Structural Biology.
[82] Ilya A. Balabin,et al. Dynamically controlled protein tunneling paths in photosynthetic reaction centers. , 2000, Science.
[83] C. Costa,et al. The Structure of an Electron Transfer Complex Containing a Cytochrome c and a Peroxidase* , 1999, The Journal of Biological Chemistry.
[84] M. Perutz,et al. The structure of haemoglobin - VI. Fourier projections on the 010 plane , 1954, Proceedings of the Royal Society of London. Series A. Mathematical and Physical Sciences.
[85] W. Braun,et al. Rapid calculation of first and second derivatives of conformational energy with respect to dihedral angles for proteins general recurrent equations , 1984, Comput. Chem..
[86] R. Abagyan,et al. Soft protein–protein docking in internal coordinates , 2002, Protein science : a publication of the Protein Society.
[87] Nancy A. Blumenstock. The Chicago Manual of Style . By the University of Chicago Press. 13th ed. Chicago: University of Chicago Press, 1982. ix, 740 pp. Glossary of Technical Terms, Bibliography, Index. $25. , 1984, Journal of Asian Studies.
[88] David Corne,et al. Evolutionary Computation In Bioinformatics , 2003 .
[89] M J Sternberg,et al. Side‐chain conformational entropy in protein folding , 1995, Protein science : a publication of the Protein Society.
[90] M. Trosset,et al. Combining Constraint Programming and Multidimensional Scaling to solve Distance Geometry Problems , 2003 .
[91] Thomas Szyperski,et al. Reduced-dimensionality NMR spectroscopy for high-throughput protein resonance assignment , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[92] William H. Press,et al. Numerical recipes in C , 2002 .
[93] J Deisenhofer,et al. X-ray structure analysis of a membrane protein complex. Electron density map at 3 A resolution and a model of the chromophores of the photosynthetic reaction center from Rhodopseudomonas viridis. , 1984, Journal of molecular biology.
[94] Ruth Nussinov,et al. Principles of docking: An overview of search algorithms and a guide to scoring functions , 2002, Proteins.
[95] M. Fillat,et al. Site-specific mutagenesis demonstrates that the structural requirements for efficient electron transfer in Anabaena ferredoxin and flavodoxin are highly dependent on the reaction partner: kinetic studies with photosystem I, ferredoxin:NADP+ reductase, and cytochrome c. , 1995, Archives of biochemistry and biophysics.
[96] Ruth Nussinov,et al. Taking geometry to its edge: Fast unbound rigid (and hinge‐bent) docking , 2003, Proteins.
[97] Glenn A. Kramer. Solving geometric constraint systems a case study in kinematics , 1992, Comput. Aided Des..
[98] J. Abrahams,et al. Crystallization of F1-ATPase from bovine heart mitochondria. , 1993, Journal of molecular biology.
[99] Christian Bessiere,et al. Arc-Consistency and Arc-Consistency Again , 1993, Artif. Intell..
[100] David S. Goodsell,et al. Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4 , 1996, J. Comput. Aided Mol. Des..
[101] M. Sternberg,et al. Rapid refinement of protein interfaces incorporating solvation: application to the docking problem. , 1998, Journal of molecular biology.
[102] E. Katchalski‐Katzir,et al. Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. , 1992, Proceedings of the National Academy of Sciences of the United States of America.
[103] M. Y. Liu,et al. Purification and characterization of desulfoferrodoxin. A novel protein from Desulfovibrio desulfuricans (ATCC 27774) and from Desulfovibrio vulgaris (strain Hildenborough) that contains a distorted rubredoxin center and a mononuclear ferrous center. , 1990, The Journal of biological chemistry.
[104] R Abagyan,et al. Homology modeling with internal coordinate mechanics: Deformation zone mapping and improvements of models via conformational search , 1997, Proteins.
[105] R. Huber,et al. Crystal structure and mechanism of CO dehydrogenase, a molybdo iron-sulfur flavoprotein containing S-selanylcysteine. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[106] R. Fraser. The structure of deoxyribose nucleic acid. , 2004, Journal of structural biology.
[107] K. Wüthrich,et al. Torsion angle dynamics for NMR structure calculation with the new program DYANA. , 1997, Journal of molecular biology.
[108] G. Tollin,et al. Structure-function relationships in Anabaena ferredoxin: correlations between X-ray crystal structures, reduction potentials, and rate constants of electron transfer to ferredoxin:NADP+ reductase for site-specific ferredoxin mutants. , 1997, Biochemistry.
[109] E. Stavridi,et al. Hydrophobic side‐chain size is a determinant of the three‐dimensional structure of the p53 oligomerization domain , 1997, The EMBO journal.
[110] Christian Bessiere,et al. Using Constraint Metaknowledge to Reduce Arc Consistency Computation , 1999, Artif. Intell..
[111] S. Grissmer,et al. Structure of the BgK-Kv1.1 Complex Based on Distance Restraints Identified by Double Mutant Cycles , 2002, The Journal of Biological Chemistry.
[112] Robert M. Haralick,et al. Increasing Tree Search Efficiency for Constraint Satisfaction Problems , 1979, Artif. Intell..
[113] David L. Waltz,et al. Understanding Line drawings of Scenes with Shadows , 1975 .
[114] V. Fülöp,et al. Desulfoferrodoxin structure determined by MAD phasing and refinement to 1.9-Å resolution reveals a unique combination of a tetrahedral FeS4 centre with a square pyramidal FeSN4 centre , 1997, JBIC Journal of Biological Inorganic Chemistry.
[115] A. Lesk,et al. The relation between the divergence of sequence and structure in proteins. , 1986, The EMBO journal.
[116] Y. Pétillot,et al. Refined X-ray structures of the oxidized, at 1.3 A, and reduced, at 1.17 A, [2Fe-2S] ferredoxin from the cyanobacterium Anabaena PCC7119 show redox-linked conformational changes. , 1999, Biochemistry.
[117] P. Kollman,et al. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? , 2000 .
[118] Andrea Bernini,et al. Biochemical filtering of a protein-protein docking simulation identifies the structure of a complex between a recombinant antibody fragment and alpha-bungarotoxin. , 2003, The Biochemical journal.
[119] David S. Goodsell,et al. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function , 1998 .
[120] B Honig,et al. Electrostatic contributions to protein–protein interactions: Fast energetic filters for docking and their physical basis , 2001, Protein science : a publication of the Protein Society.
[121] Torsten Herrmann,et al. Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. , 2002, Journal of molecular biology.
[122] M J Sternberg,et al. New algorithm to model protein-protein recognition based on surface complementarity. Applications to antibody-antigen docking. , 1992, Journal of molecular biology.
[123] G. G. Stokes. "J." , 1890, The New Yale Book of Quotations.
[124] Pedro Barahona,et al. Propagating N-Ary Rigid-Body Constraints , 2003, CP.
[125] R. L. Trask. The Penguin Guide To Punctuation , 2004 .
[126] Rolf Backofen,et al. Application of constraint programming techniques for structure prediction of lattice proteins with extended alphabets , 1999, Bioinform..
[127] Stuart James,et al. The Chicago Manual of Style (15th edition) , 2005 .
[128] C Kooperberg,et al. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. , 1997, Journal of molecular biology.
[129] Sebastian Doniach,et al. Protein structure prediction constrained by solution X-ray scattering data and structural homology identification. , 2002, Journal of molecular biology.
[130] Robert Rodosek. A Constraint-Based Approach for Deriving 3-D Structures of Cyclic Polypeptides , 2004, Constraints.
[131] R. Huber,et al. Crystal structure of three consecutive laminin-type epidermal growth factor-like (LE) modules of laminin gamma1 chain harboring the nidogen binding site. , 1996, Journal of molecular biology.
[132] D. le Coq,et al. Crystal structure of an activated form of the PTS regulation domain from the LicT transcriptional antiterminator , 2001, The EMBO journal.
[133] R. Backofen,et al. Protein similarity search under mRNA structural constraints: application to targeted selenocysteine insertion. , 2002, In silico biology.
[134] E. H ckel,et al. Zur Theorie der Elektrolyte , 1924 .
[135] Chris Bailey-Kellogg,et al. The NOESY Jigsaw: Automated Protein Secondary Structure and Main-Chain Assignment from Sparse, Unassigned NMR Data , 2000, J. Comput. Biol..
[136] I. Moura,et al. NMR determination of the global structure of the 113Cd derivative of desulforedoxin: Investigation of the hydrogen bonding pattern at the metal center , 1998, Protein science : a publication of the Protein Society.
[137] P. Kollman,et al. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. , 1998, Science.
[138] Alexander Bockmayr,et al. Direct phasing by binary integer programming. , 2002, Acta crystallographica. Section A, Foundations of crystallography.
[139] Sanjay Bhansali,et al. A Principled Approach Towards Symbolic Geometric Constraint Satisfaction , 1996, J. Artif. Intell. Res..
[140] J. Tukey,et al. An algorithm for the machine calculation of complex Fourier series , 1965 .
[141] Sandor Vajda,et al. CAPRI: A Critical Assessment of PRedicted Interactions , 2003, Proteins.
[142] B. Todd,et al. Connecting nanoscale images of proteins with their genetic sequences. , 2003, Biophysical journal.
[143] M. Sternberg,et al. An analysis of conformational changes on protein-protein association: implications for predictive docking. , 1999, Protein engineering.
[144] Zhiping Weng,et al. Docking unbound proteins using shape complementarity, desolvation, and electrostatics , 2002, Proteins.
[145] Kersten S. Rabe,et al. The Ternary Complex of Cytochrome f and Cytochrome c: Identification of a Second Binding Site and Competition for Plastocyanin Binding , 2002, Chembiochem : a European journal of chemical biology.
[146] P. Argos,et al. Seventy‐five percent accuracy in protein secondary structure prediction , 1997, Proteins.
[147] H. W. Fowler. A Dictionary of Modern English Usage , 1926 .
[148] Berthold K. P. Horn,et al. Closed-form solution of absolute orientation using unit quaternions , 1987 .
[149] Pedro Barahona,et al. Applying Constraint Programming to Protein Structure Determination , 1999, CP.
[150] Hui Zhang,et al. A new computational model for protein folding based on atomic solvation , 1995, Protein science : a publication of the Protein Society.
[151] L. Delbaere,et al. The 2.0-A resolution structure of Escherichia coli histidine-containing phosphocarrier protein HPr. A redetermination. , 1994, The Journal of biological chemistry.
[152] Michael W. Trosset,et al. Distance Matrix Completion by Numerical Optimization , 2000, Comput. Optim. Appl..
[153] Lode Wyns,et al. Three Camelid VHH Domains in Complex with Porcine Pancreatic α-Amylase , 2002, The Journal of Biological Chemistry.
[154] Jorge Nocedal,et al. Algorithm 778: L-BFGS-B: Fortran subroutines for large-scale bound-constrained optimization , 1997, TOMS.
[155] M Czjzek,et al. Structural Model of the Fe-Hydrogenase/Cytochromec 553 Complex Combining Transverse Relaxation-optimized Spectroscopy Experiments and Soft Docking Calculations* , 2000, The Journal of Biological Chemistry.
[156] P. Colman,et al. Three-dimensional structures of two plant beta-glucan endohydrolases with distinct substrate specificities. , 1994, Proceedings of the National Academy of Sciences of the United States of America.
[157] R J Read,et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. , 1998, Acta crystallographica. Section D, Biological crystallography.
[158] William Thomas Astbury,et al. X-Ray Studies of the Structure of Hair, Wool, and Related Fibres. I. General , 1932 .