Published in Curr Opin Struct Biol on April 01, 2004
Statistical potential for assessment and prediction of protein structures. Protein Sci (2006) 8.98
MetaMQAP: a meta-server for the quality assessment of protein models. BMC Bioinformatics (2008) 1.88
OPUS-PSP: an orientation-dependent statistical all-atom potential derived from side-chain packing. J Mol Biol (2007) 1.48
GOAP: a generalized orientation-dependent, all-atom statistical potential for protein structure prediction. Biophys J (2011) 1.39
OPUS-Ca: a knowledge-based potential function requiring only Calpha positions. Protein Sci (2007) 1.33
Lessons from the design of a novel atomic potential for protein folding. Protein Sci (2005) 1.02
Statistical potential for modeling and ranking of protein-ligand interactions. J Chem Inf Model (2011) 0.95
A coarse-grained potential for fold recognition and molecular dynamics simulations of proteins. Proteins (2009) 0.95
Multiscale coarse-graining of the protein energy landscape. PLoS Comput Biol (2010) 0.93
Quantitative prediction of protein-protein binding affinity with a potential of mean force considering volume correction. Protein Sci (2009) 0.93
Potentials of mean force for protein structure prediction vindicated, formalized and generalized. PLoS One (2010) 0.93
Further optimization of a hybrid united-atom and coarse-grained force field for folding simulations: Improved backbone hydration and interactions between charged side chains. J Chem Theory Comput (2012) 0.90
Sequence composition and environment effects on residue fluctuations in protein structures. J Chem Phys (2010) 0.90
Scoring predictive models using a reduced representation of proteins: model and energy definition. BMC Struct Biol (2007) 0.90
Full cyclic coordinate descent: solving the protein loop closure problem in Calpha space. BMC Bioinformatics (2005) 0.89
A free-rotating and self-avoiding chain model for deriving statistical potentials based on protein structures. Biophys J (2007) 0.87
FIEFDom: a transparent domain boundary recognition system using a fuzzy mean operator. Nucleic Acids Res (2008) 0.87
Four distances between pairs of amino acids provide a precise description of their interaction. PLoS Comput Biol (2009) 0.86
Computational and experimental approaches to reveal the effects of single nucleotide polymorphisms with respect to disease diagnostics. Int J Mol Sci (2014) 0.86
Energy functions in de novo protein design: current challenges and future prospects. Annu Rev Biophys (2013) 0.84
Protein structure modelling and evaluation based on a 4-distance description of side-chain interactions. BMC Bioinformatics (2010) 0.83
Protein folding in a reverse micelle environment: the role of confinement and dehydration. J Chem Phys (2011) 0.82
Recovering physical potentials from a model protein databank. Proc Natl Acad Sci U S A (2010) 0.80
A quality metric for homology modeling: the H-factor. BMC Bioinformatics (2011) 0.80
COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids. J Chem Theory Comput (2014) 0.80
The hydrophobic temperature dependence of amino acids directly calculated from protein structures. PLoS Comput Biol (2015) 0.80
A contact energy function considering residue hydrophobic environment and its application in protein fold recognition. Genomics Proteomics Bioinformatics (2005) 0.77
ROTAS: a rotamer-dependent, atomic statistical potential for assessment and prediction of protein structures. BMC Bioinformatics (2014) 0.75
Thermodynamics of Hydrophobic Amino Acids in Solution: A Combined Experimental-Computational Study. J Phys Chem Lett (2016) 0.75
modPDZpep: a web resource for structure based analysis of human PDZ-mediated interaction networks. Biol Direct (2016) 0.75
Navigating the folding routes. Science (1995) 7.34
Metastability of the folded states of globular proteins. Proc Natl Acad Sci U S A (1990) 3.79
Molecular crowding enhances native state stability and refolding rates of globular proteins. Proc Natl Acad Sci U S A (2005) 3.29
Dissecting the assembly of Abeta16-22 amyloid peptides into antiparallel beta sheets. Structure (2003) 3.18
Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence-dependent properties. Fold Des (1997) 3.14
Kinetics and thermodynamics of folding in model proteins. Proc Natl Acad Sci U S A (1993) 3.08
The nature of folded states of globular proteins. Biopolymers (1992) 2.91
Mechanisms and kinetics of beta-hairpin formation. Proc Natl Acad Sci U S A (2000) 2.66
Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes. Protein Sci (1999) 2.41
Folding of RNA involves parallel pathways. J Mol Biol (1997) 2.22
Native topology determines force-induced unfolding pathways in globular proteins. Proc Natl Acad Sci U S A (2000) 2.09
Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding. Proc Natl Acad Sci U S A (2008) 2.03
Monomer adds to preformed structured oligomers of Abeta-peptides by a two-stage dock-lock mechanism. Proc Natl Acad Sci U S A (2006) 2.01
Simulations of beta-hairpin folding confined to spherical pores using distributed computing. Proc Natl Acad Sci U S A (2002) 1.99
Kinetics and thermodynamics of folding of a de novo designed four-helix bundle protein. J Mol Biol (1996) 1.95
Novel methods of sampling phase space in the simulation of biological systems. Curr Opin Struct Biol (1997) 1.93
Interactions between hydrophobic and ionic solutes in aqueous guanidinium chloride and urea solutions: lessons for protein denaturation mechanism. J Am Chem Soc (2007) 1.90
Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations. Proc Natl Acad Sci U S A (2006) 1.90
Dynamics of allosteric transitions in GroEL. Proc Natl Acad Sci U S A (2006) 1.88
Exploring the kinetic requirements for enhancement of protein folding rates in the GroEL cavity. J Mol Biol (1999) 1.85
Chaperonin-facilitated protein folding: optimization of rate and yield by an iterative annealing mechanism. Proc Natl Acad Sci U S A (1996) 1.79
Role of counterion condensation in folding of the Tetrahymena ribozyme. I. Equilibrium stabilization by cations. J Mol Biol (2001) 1.78
Exploring protein aggregation and self-propagation using lattice models: phase diagram and kinetics. Protein Sci (2002) 1.77
Can energy landscape roughness of proteins and RNA be measured by using mechanical unfolding experiments? Proc Natl Acad Sci U S A (2003) 1.76
Revealing the bifurcation in the unfolding pathways of GFP by using single-molecule experiments and simulations. Proc Natl Acad Sci U S A (2007) 1.74
Theoretical predictions of folding pathways by using the proximity rule, with applications to bovine pancreatic trypsin inhibitor. Proc Natl Acad Sci U S A (1995) 1.73
Dynamics of Asp23-Lys28 salt-bridge formation in Abeta10-35 monomers. J Am Chem Soc (2006) 1.63
Multiple protein folding nuclei and the transition state ensemble in two-state proteins. Proteins (2001) 1.61
Role of counterion condensation in folding of the Tetrahymena ribozyme. II. Counterion-dependence of folding kinetics. J Mol Biol (2001) 1.61
Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved. Structure (2005) 1.60
Dynamics of unbinding of cell adhesion molecules: transition from catch to slip bonds. Proc Natl Acad Sci U S A (2005) 1.59
Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins. Structure (2006) 1.58
Mechanical unfolding of RNA hairpins. Proc Natl Acad Sci U S A (2005) 1.57
Charge density of divalent metal cations determines RNA stability. J Am Chem Soc (2007) 1.56
Effects of denaturants and osmolytes on proteins are accurately predicted by the molecular transfer model. Proc Natl Acad Sci U S A (2008) 1.52
Lattice models for proteins reveal multiple folding nuclei for nucleation-collapse mechanism. J Mol Biol (1998) 1.50
Simulation study of the structure and dynamics of the Alzheimer's amyloid peptide congener in solution. Biophys J (2001) 1.45
Molecular dynamics simulations of end-to-end contact formation in hydrocarbon chains in water and aqueous urea solution. J Am Chem Soc (2003) 1.44
Toward a molecular theory of early and late events in monomer to amyloid fibril formation. Annu Rev Phys Chem (2011) 1.43
Forced-unfolding and force-quench refolding of RNA hairpins. Biophys J (2006) 1.42
Collapse transition in proteins. Phys Chem Chem Phys (2008) 1.41
Stretching single-domain proteins: phase diagram and kinetics of force-induced unfolding. Proc Natl Acad Sci U S A (1999) 1.41
Magnesium-dependent folding of self-splicing RNA: exploring the link between cooperativity, thermodynamics, and kinetics. Proc Natl Acad Sci U S A (1999) 1.38
Rigor to post-rigor transition in myosin V: link between the dynamics and the supporting architecture. Structure (2010) 1.37
Energy landscape theory for Alzheimer's amyloid beta-peptide fibril elongation. Proteins (2001) 1.37
Ribosome exit tunnel can entropically stabilize alpha-helices. Proc Natl Acad Sci U S A (2005) 1.36
RNA tertiary interactions mediate native collapse of a bacterial group I ribozyme. J Mol Biol (2005) 1.36
Determination of network of residues that regulate allostery in protein families using sequence analysis. Protein Sci (2006) 1.35
Cooperativity in protein folding: from lattice models with sidechains to real proteins. Fold Des (1998) 1.34
Aqueous urea solution destabilizes Abeta(16-22) oligomers. Proc Natl Acad Sci U S A (2004) 1.34
Force-dependent hopping rates of RNA hairpins can be estimated from accurate measurement of the folding landscapes. Proc Natl Acad Sci U S A (2008) 1.33
Capturing the essence of folding and functions of biomolecules using coarse-grained models. Nat Commun (2011) 1.32
Multiple stepwise refolding of immunoglobulin domain I27 upon force quench depends on initial conditions. Proc Natl Acad Sci U S A (2005) 1.32
Exploring the energy landscape in proteins. Proc Natl Acad Sci U S A (1993) 1.32
Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations. Biophys J (2007) 1.31
Size, shape, and flexibility of RNA structures. J Chem Phys (2006) 1.31
Probing the instabilities in the dynamics of helical fragments from mouse PrPC. Proc Natl Acad Sci U S A (2004) 1.31
Mechanical unfolding of RNA: from hairpins to structures with internal multiloops. Biophys J (2006) 1.27
Compaction of a bacterial group I ribozyme coincides with the assembly of core helices. Biochemistry (2004) 1.26
Relative stability of helices determines the folding landscape of adenine riboswitch aptamers. J Am Chem Soc (2008) 1.24
Vibrational population relaxation of carbon monoxide in the heme pocket of photolyzed carbonmonoxy myoglobin: comparison of time-resolved mid-IR absorbance experiments and molecular dynamics simulations. Proc Natl Acad Sci U S A (1999) 1.24
Persistence length changes dramatically as RNA folds. Phys Rev Lett (2005) 1.23
Folding of the Tetrahymena ribozyme by polyamines: importance of counterion valence and size. J Mol Biol (2004) 1.23
Allosteric communication in dihydrofolate reductase: signaling network and pathways for closed to occluded transition and back. J Mol Biol (2007) 1.22
Extracting stacking interaction parameters for RNA from the data set of native structures. J Mol Biol (2005) 1.22
Nanopore-protein interactions dramatically alter stability and yield of the native state in restricted spaces. J Mol Biol (2006) 1.22
Metal ion dependence of cooperative collapse transitions in RNA. J Mol Biol (2009) 1.20
Effects of crowding and confinement on the structures of the transition state ensemble in proteins. J Phys Chem B (2007) 1.20
Symmetric connectivity of secondary structure elements enhances the diversity of folding pathways. J Mol Biol (2005) 1.19
Charge states rather than propensity for beta-structure determine enhanced fibrillogenesis in wild-type Alzheimer's beta-amyloid peptide compared to E22Q Dutch mutant. Protein Sci (2002) 1.19
Kinetics of peptide folding: computer simulations of SYPFDV and peptide variants in water. J Mol Biol (1997) 1.18
Factors governing the foldability of proteins. Proteins (1996) 1.18
Assembly mechanisms of RNA pseudoknots are determined by the stabilities of constituent secondary structures. Proc Natl Acad Sci U S A (2009) 1.16
Stiffness of the distal loop restricts the structural heterogeneity of the transition state ensemble in SH3 domains. J Mol Biol (2002) 1.16
Dynamics of locking of peptides onto growing amyloid fibrils. Proc Natl Acad Sci U S A (2009) 1.15
A study of vibrational relaxation of B-state carbon monoxide in the heme pocket of photolyzed carboxymyoglobin. Biophys J (1999) 1.14
Virtual atom representation of hydrogen bonds in minimal off-lattice models of alpha helices: effect on stability, cooperativity and kinetics. Fold Des (1998) 1.14
Multiple probes are required to explore and control the rugged energy landscape of RNA hairpins. J Am Chem Soc (2008) 1.13
Probing the initial stage of aggregation of the Abeta(10-35)-protein: assessing the propensity for peptide dimerization. J Mol Biol (2004) 1.12
Dynamic transition in tRNA is solvent induced. J Am Chem Soc (2006) 1.11
From mechanical folding trajectories to intrinsic energy landscapes of biopolymers. Proc Natl Acad Sci U S A (2013) 1.10
Kinetics of loop formation in polymer chains. J Phys Chem B (2008) 1.10
Annealing function of GroEL: structural and bioinformatic analysis. Biophys Chem (2003) 1.10
Compression and stretching of a self-avoiding chain in cylindrical nanopores. Phys Rev Lett (2008) 1.09
Entropic stabilization of proteins by TMAO. J Phys Chem B (2011) 1.09
Probing the mechanisms of fibril formation using lattice models. J Chem Phys (2008) 1.08
Kinetics of interior loop formation in semiflexible chains. J Chem Phys (2006) 1.08
Influence of preformed Asp23-Lys28 salt bridge on the conformational fluctuations of monomers and dimers of Abeta peptides with implications for rates of fibril formation. J Phys Chem B (2009) 1.08
Counterion charge density determines the position and plasticity of RNA folding transition states. J Mol Biol (2006) 1.07
Probing the origins of increased activity of the E22Q "Dutch" mutant Alzheimer's beta-amyloid peptide. Biophys J (2001) 1.06
Minimal models for proteins and RNA from folding to function. Prog Mol Biol Transl Sci (2008) 1.05
Refolding dynamics of stretched biopolymers upon force quench. Proc Natl Acad Sci U S A (2009) 1.04
Interactions between amino acid side chains in cylindrical hydrophobic nanopores with applications to peptide stability. Proc Natl Acad Sci U S A (2008) 1.04
Transmembrane structures of amyloid precursor protein dimer predicted by replica-exchange molecular dynamics simulations. J Am Chem Soc (2009) 1.04
Modeling the role of disulfide bonds in protein folding: entropic barriers and pathways. Proteins (1995) 1.04
Factors governing fibrillogenesis of polypeptide chains revealed by lattice models. Phys Rev Lett (2010) 1.03
Allostery wiring diagrams in the transitions that drive the GroEL reaction cycle. J Mol Biol (2008) 1.03
Effect of finite size on cooperativity and rates of protein folding. J Phys Chem A (2006) 1.03