Published in Structure on October 01, 2007
Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr (2004) 227.01
Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr (1998) 169.28
How to measure and predict the molar absorption coefficient of a protein. Protein Sci (1995) 18.71
The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding. J Mol Biol (1992) 6.10
Mapping the transition state and pathway of protein folding by protein engineering. Nature (1989) 5.44
Denatured states of proteins. Annu Rev Biochem (1991) 4.86
Experimental and theoretical aspects of protein folding. Adv Protein Chem (1975) 3.51
Im7 folding mechanism: misfolding on a path to the native state. Nat Struct Biol (2002) 3.15
Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain. Nat Struct Biol (1998) 3.02
NMR determination of residual structure in a urea-denatured protein, the 434-repressor. Science (1992) 2.83
Engineered disulfide bonds as probes of the folding pathway of barnase: increasing the stability of proteins against the rate of denaturation. Biochemistry (1993) 2.61
Structure of the transition state for the folding/unfolding of the barley chymotrypsin inhibitor 2 and its implications for mechanisms of protein folding. Proc Natl Acad Sci U S A (1994) 2.59
Structure of phosphate-free ribonuclease A refined at 1.26 A. Biochemistry (1988) 2.53
The folding of an enzyme. III. Structure of the transition state for unfolding of barnase analysed by a protein engineering procedure. J Mol Biol (1992) 2.34
Negative activation enthalpies in the kinetics of protein folding. Proc Natl Acad Sci U S A (1995) 2.24
NMR structural and dynamic characterization of the acid-unfolded state of apomyoglobin provides insights into the early events in protein folding. Biochemistry (2001) 2.07
Disulfide bonds and protein folding. Biochemistry (2000) 2.03
The energy landscape of a fast-folding protein mapped by Ala-->Gly substitutions. Nat Struct Biol (1997) 1.90
Structure of the transition state for folding of the 129 aa protein CheY resembles that of a smaller protein, CI-2. Fold Des (1996) 1.90
Acid catalysis of the formation of the slow-folding species of RNase A: evidence that the reaction is proline isomerization. Proc Natl Acad Sci U S A (1978) 1.78
Native proteins are surface-molten solids: application of the Lindemann criterion for the solid versus liquid state. J Mol Biol (1999) 1.68
Structural characterization of the FK506 binding protein unfolded in urea and guanidine hydrochloride. J Mol Biol (1994) 1.58
Equilibrium NMR studies of unfolded and partially folded proteins. Nat Struct Biol (1998) 1.51
Different folding transition states may result in the same native structure. Nat Struct Biol (1996) 1.50
Structure of the transition state in the folding process of human procarboxypeptidase A2 activation domain. J Mol Biol (1998) 1.47
Thermodynamic properties of an extremely rapid protein folding reaction. Biochemistry (1996) 1.45
Molecular hinges in protein folding: the urea-denatured state of apomyoglobin. Biochemistry (2002) 1.35
Characterizing the protein folding transition state using psi analysis. Chem Rev (2006) 1.33
Differences in the folding transition state of ubiquitin indicated by phi and psi analyses. Proc Natl Acad Sci U S A (2004) 1.30
A comparison of the pH, urea, and temperature-denatured states of barnase by heteronuclear NMR: implications for the initiation of protein folding. J Mol Biol (1995) 1.30
Distributions of intramolecular distances in the reduced and denatured states of bovine pancreatic ribonuclease A. Folding initiation structures in the C-terminal portions of the reduced protein. Biochemistry (2001) 1.20
Conformational stability is a determinant of ribonuclease A cytotoxicity. J Biol Chem (2000) 1.16
Influence of an extrinsic cross-link on the folding pathway of ribonuclease A. Conformational and thermodynamic analysis of cross-linked (lysine7-lysine41)-ribonuclease a. Biochemistry (1984) 1.16
Analysis of the structure of ribonuclease A in native and partially denatured states by time-resolved noradiative dynamic excitation energy transfer between site-specific extrinsic probes. Biochemistry (1995) 1.15
Regeneration of bovine pancreatic ribonuclease A. 1. Steady-state distribution. Biochemistry (1993) 1.08
Denaturant-induced movement of the transition state of protein folding revealed by high-pressure stopped-flow measurements. Proc Natl Acad Sci U S A (2000) 1.07
Folding and unfolding kinetics of the proline-to-alanine mutants of bovine pancreatic ribonuclease A. Biochemistry (1996) 1.07
Expression of wild-type and mutant bovine pancreatic ribonuclease A in Escherichia coli. Proc Natl Acad Sci U S A (1993) 1.01
Conformational studies of a peptide corresponding to a region of the C-terminus of ribonuclease A: implications as a potential chain-folding initiation site. Biochemistry (1991) 1.00
The limited digestion of ribonuclease with pepsin. J Biol Chem (1956) 0.96
Effect of preformed correct tertiary interactions on rapid two-state tendamistat folding: evidence for hairpins as initiation sites for beta-sheet formation. Biochemistry (1997) 0.96
Nonlocal interactions stabilize long range loops in the initial folding intermediates of reduced bovine pancreatic trypsin inhibitor. Biochemistry (1995) 0.93
Nature of the unfolded state of ribonuclease A: effect of cis-trans X-Pro peptide bond isomerization. Biochemistry (1996) 0.93
Preliminary crystallographic data for cross-linked (lysine7-lysine41)-ribonuclease A. J Mol Biol (1985) 0.92
Structure of a hydrophobically collapsed intermediate on the conformational folding pathway of ribonuclease A probed by hydrogen-deuterium exchange. Biochemistry (1996) 0.90
Structural examination of phi-value analysis in protein folding. Biochemistry (2004) 0.89
An intermediate seeks instant gratification. Nat Struct Biol (2002) 0.85
Intrinsic stabilities of portions of the ribonuclease molecule. Biochemistry (1980) 0.82
Local structure involving histidine-12 in reduced S-sulfonated ribonuclease A detected by proton NMR spectroscopy under folding conditions. Proc Natl Acad Sci U S A (1984) 0.80
Influence of an extrinsic cross-link on the folding pathway of ribonuclease A. Kinetics of folding-unfolding. Biochemistry (1985) 0.79
Folding of ribonuclease, S-protein, and des(121-124)-ribonuclease during glutathione oxidation of the reduced proteins. Biochemistry (1980) 0.78
Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains. Proc Natl Acad Sci U S A (2005) 2.85
The structural and biochemical foundations of thiamin biosynthesis. Annu Rev Biochem (2009) 2.32
Insufficiently dehydrated hydrogen bonds as determinants of protein interactions. Proc Natl Acad Sci U S A (2002) 2.20
Reconstitution of ThiC in thiamine pyrimidine biosynthesis expands the radical SAM superfamily. Nat Chem Biol (2008) 1.96
Diphthamide biosynthesis requires an organic radical generated by an iron-sulphur enzyme. Nature (2010) 1.85
An atomically detailed study of the folding pathways of protein A with the stochastic difference equation. Proc Natl Acad Sci U S A (2002) 1.76
Proline cis-trans isomerization and protein folding. Biochemistry (2002) 1.76
Molecular dynamics with the united-residue model of polypeptide chains. I. Lagrange equations of motion and tests of numerical stability in the microcanonical mode. J Phys Chem B (2005) 1.71
Effects of side-chain orientation on the 13C chemical shifts of antiparallel beta-sheet model peptides. J Biomol NMR (2006) 1.71
Structural analyses reveal two distinct families of nucleoside phosphorylases. Biochem J (2002) 1.69
Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model alpha-helical systems. J Phys Chem B (2005) 1.69
A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: application to the UNRES force field. Proc Natl Acad Sci U S A (2002) 1.64
Molecular origin of anticooperativity in hydrophobic association. J Phys Chem B (2005) 1.62
Quantum-mechanics-derived 13Calpha chemical shift server (CheShift) for protein structure validation. Proc Natl Acad Sci U S A (2009) 1.59
Predicting 13Calpha chemical shifts for validation of protein structures. J Biomol NMR (2007) 1.59
Folding of the villin headpiece subdomain from random structures. Analysis of the charge distribution as a function of pH. J Mol Biol (2004) 1.58
Polyproline II conformation is one of many local conformational states and is not an overall conformation of unfolded peptides and proteins. Proc Natl Acad Sci U S A (2006) 1.57
Computational techniques for efficient conformational sampling of proteins. Curr Opin Struct Biol (2008) 1.54
Structure of human phosphopantothenoylcysteine synthetase at 2.3 A resolution. Structure (2003) 1.54
Atomic structure of the KEOPS complex: an ancient protein kinase-containing molecular machine. Mol Cell (2008) 1.51
Saccharomyces cerevisiae THI4p is a suicide thiamine thiazole synthase. Nature (2011) 1.50
Quantum chemical 13C(alpha) chemical shift calculations for protein NMR structure determination, refinement, and validation. Proc Natl Acad Sci U S A (2008) 1.50
Structure of HHARI, a RING-IBR-RING ubiquitin ligase: autoinhibition of an Ariadne-family E3 and insights into ligation mechanism. Structure (2013) 1.48
The role of hydrophobic interactions in initiation and propagation of protein folding. Proc Natl Acad Sci U S A (2006) 1.42
Principal component analysis for protein folding dynamics. J Mol Biol (2008) 1.42
Structure of the Escherichia coli ThiS-ThiF complex, a key component of the sulfur transfer system in thiamin biosynthesis. Biochemistry (2006) 1.42
Towards crystal structure prediction of complex organic compounds--a report on the fifth blind test. Acta Crystallogr B (2011) 1.40
Flavogenomics--a genomic and structural view of flavin-dependent proteins. FEBS J (2011) 1.40
Atomically detailed folding simulation of the B domain of staphylococcal protein A from random structures. Proc Natl Acad Sci U S A (2003) 1.40
Structure of oxalate decarboxylase from Bacillus subtilis at 1.75 A resolution. Biochemistry (2002) 1.39
Crystal structure of 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase from Salmonella typhimurium at 2.3 A resolution. Structure (2002) 1.39
Atg8 transfer from Atg7 to Atg3: a distinctive E1-E2 architecture and mechanism in the autophagy pathway. Mol Cell (2011) 1.38
Structural biology of enzymes of the thiamin biosynthesis pathway. Curr Opin Struct Biol (2003) 1.37
Structural and mechanistic studies on ThiO, a glycine oxidase essential for thiamin biosynthesis in Bacillus subtilis. Biochemistry (2003) 1.35
Significant progress in predicting the crystal structures of small organic molecules--a report on the fourth blind test. Acta Crystallogr B (2009) 1.29
Crystal structure and mechanism of tryptophan 2,3-dioxygenase, a heme enzyme involved in tryptophan catabolism and in quinolinate biosynthesis. Biochemistry (2007) 1.29
Biosynthesis of thiamin thiazole in eukaryotes: conversion of NAD to an advanced intermediate. J Am Chem Soc (2007) 1.29
Stepwise deamidation of ribonuclease A at five sites determined by top down mass spectrometry. Biochemistry (2006) 1.28
Replica Exchange and Multicanonical Algorithms with the coarse-grained UNRES force field. J Chem Theory Comput (2006) 1.27
Mechanism of ubiquitin ligation and lysine prioritization by a HECT E3. Elife (2013) 1.27
Addition of side chains to a known backbone with defined side-chain centroids. Biophys Chem (2003) 1.27
Structural characterization of the regulatory proteins TenA and TenI from Bacillus subtilis and identification of TenA as a thiaminase II. Biochemistry (2005) 1.25
Kinetic studies of folding of the B-domain of staphylococcal protein A with molecular dynamics and a united-residue (UNRES) model of polypeptide chains. J Mol Biol (2005) 1.25
Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. 2. Tests with simple spherical systems. J Phys Chem B (2007) 1.23
Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field. J Comput Chem (2009) 1.22
Structural insights into the function of the thiamin biosynthetic enzyme Thi4 from Saccharomyces cerevisiae. Biochemistry (2006) 1.20
Enzymatic reactions involving novel mechanisms of carbanion stabilization. Curr Opin Chem Biol (2004) 1.20
Thiamin biosynthesis in eukaryotes: characterization of the enzyme-bound product of thiazole synthase from Saccharomyces cerevisiae and its implications in thiazole biosynthesis. J Am Chem Soc (2006) 1.19
Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field. J Phys Chem A (2010) 1.19
Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with alpha and alpha+beta Proteins. J Chem Theory Comput (2009) 1.19
A RING E3-substrate complex poised for ubiquitin-like protein transfer: structural insights into cullin-RING ligases. Nat Struct Mol Biol (2011) 1.18
Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. IV. Pairs of different hydrophobic side chains. J Phys Chem B (2008) 1.15
Energy-based reconstruction of a protein backbone from its alpha-carbon trace by a Monte-Carlo method. J Comput Chem (2002) 1.15
Factors affecting the use of 13C(alpha) chemical shifts to determine, refine, and validate protein structures. Proteins (2008) 1.14
Structural basis for substrate specificity of Escherichia coli purine nucleoside phosphorylase. J Biol Chem (2003) 1.14
Sequential nearest-neighbor effects on computed 13Calpha chemical shifts. J Biomol NMR (2010) 1.14
Insights into anaphase promoting complex TPR subdomain assembly from a CDC26-APC6 structure. Nat Struct Mol Biol (2009) 1.13
Structural studies on 3-hydroxyanthranilate-3,4-dioxygenase: the catalytic mechanism of a complex oxidation involved in NAD biosynthesis. Biochemistry (2005) 1.12
Topology of Type II REases revisited; structural classes and the common conserved core. Nucleic Acids Res (2007) 1.11
Crystal structure of clustered regularly interspaced short palindromic repeats (CRISPR)-associated Csn2 protein revealed Ca2+-dependent double-stranded DNA binding activity. J Biol Chem (2011) 1.11
Assessing the accuracy of protein structures by quantum mechanical computations of 13C(alpha) chemical shifts. Acc Chem Res (2009) 1.11
Polyproline II helix conformation in a proline-rich environment: a theoretical study. Biophys J (2004) 1.10
A new force field (ECEPP-05) for peptides, proteins, and organic molecules. J Phys Chem B (2006) 1.10
Implementation of a symplectic multiple-time-step molecular dynamics algorithm, based on the united-residue mesoscopic potential energy function. J Chem Phys (2006) 1.08
An improved functional form for the temperature scaling factors of the components of the mesoscopic UNRES force field for simulations of protein structure and dynamics. J Phys Chem B (2009) 1.08
Thiamin biosynthesis in Bacillus subtilis: structure of the thiazole synthase/sulfur carrier protein complex. Biochemistry (2004) 1.07
beta-hairpin-forming peptides; models of early stages of protein folding. Biophys Chem (2010) 1.07
Evolutionary links as revealed by the structure of Thermotoga maritima S-adenosylmethionine decarboxylase. J Biol Chem (2004) 1.07
Assessing the fractions of tautomeric forms of the imidazole ring of histidine in proteins as a function of pH. Proc Natl Acad Sci U S A (2011) 1.07
How main-chains of proteins explore the free-energy landscape in native states. Proc Natl Acad Sci U S A (2008) 1.06
Structural insights into the mechanism of the PLP synthase holoenzyme from Thermotoga maritima. Biochemistry (2006) 1.05
Mechanism of human S-adenosylmethionine decarboxylase proenzyme processing as revealed by the structure of the S68A mutant. Biochemistry (2003) 1.05
Mechanism of fiber assembly: treatment of Aβ peptide aggregation with a coarse-grained united-residue force field. J Mol Biol (2010) 1.04
Use of 13Calpha chemical shifts in protein structure determination. J Phys Chem B (2007) 1.04
Cofactor biosynthesis--still yielding fascinating new biological chemistry. Curr Opin Chem Biol (2008) 1.04
Noncanonical E2 recruitment by the autophagy E1 revealed by Atg7-Atg3 and Atg7-Atg10 structures. Nat Struct Mol Biol (2012) 1.03
Structure of Toxoplasma gondii adenosine kinase in complex with an ATP analog at 1.1 angstroms resolution. Acta Crystallogr D Biol Crystallogr (2006) 1.03
Biosynthesis of the thiamin-thiazole in eukaryotes: identification of a thiazole tautomer intermediate. J Am Chem Soc (2008) 1.02
Domain organization of Salmonella typhimurium formylglycinamide ribonucleotide amidotransferase revealed by X-ray crystallography. Biochemistry (2004) 1.02
Influence of temperature, friction, and random forces on folding of the B-domain of staphylococcal protein A: all-atom molecular dynamics in implicit solvent. J Comput Chem (2007) 1.02
Crystal structure of a sulfur carrier protein complex found in the cysteine biosynthetic pathway of Mycobacterium tuberculosis. Biochemistry (2008) 1.02
Pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii: crystal structures of the self-cleaved and S53A proenzyme forms. Structure (2003) 1.01
Complexed structures of formylglycinamide ribonucleotide amidotransferase from Thermotoga maritima describe a novel ATP binding protein superfamily. Biochemistry (2006) 1.01
Packing helices in proteins by global optimization of a potential energy function. Proc Natl Acad Sci U S A (2003) 1.00
Unblocked statistical-coil tetrapeptides and pentapeptides in aqueous solution: a theoretical study. J Biomol NMR (2002) 1.00
Reconstitution and characterization of eukaryotic N6-threonylcarbamoylation of tRNA using a minimal enzyme system. Nucleic Acids Res (2013) 1.00
Further evidence for the absence of polyproline II stretch in the XAO peptide. Biophys J (2007) 1.00
O-phospho-L-serine and the thiocarboxylated sulfur carrier protein CysO-COSH are substrates for CysM, a cysteine synthase from Mycobacterium tuberculosis. Biochemistry (2008) 1.00
CNK and HYP form a discrete dimer by their SAM domains to mediate RAF kinase signaling. Proc Natl Acad Sci U S A (2008) 0.99
Molecular simulation study of cooperativity in hydrophobic association: clusters of four hydrophobic particles. Biophys Chem (2003) 0.99
Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. VI. Oppositely charged side chains. J Phys Chem B (2011) 0.99
Coarse-grained force field: general folding theory. Phys Chem Chem Phys (2011) 0.99
Performance of density functional models to reproduce observed (13)C(alpha) chemical shifts of proteins in solution. J Comput Chem (2009) 0.99
How adequate are one- and two-dimensional free energy landscapes for protein folding dynamics? Phys Rev Lett (2009) 0.99
Evidence, from simulations, of a single state with residual native structure at the thermal denaturation midpoint of a small globular protein. J Am Chem Soc (2010) 0.98