Published in RNA on April 26, 2011
The nuclear magnetic resonance of CCCC RNA reveals a right-handed helix, and revised parameters for AMBER force field torsions improve structural predictions from molecular dynamics. Biochemistry (2013) 1.02
Modeling nucleic acids. Curr Opin Struct Biol (2012) 0.98
Coarse grained models reveal essential contributions of topological constraints to the conformational free energy of RNA bulges. J Phys Chem B (2014) 0.95
The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems. Chem Soc Rev (2014) 0.88
SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction. Nucleic Acids Res (2015) 0.86
The role of nucleobase interactions in RNA structure and dynamics. Nucleic Acids Res (2014) 0.86
The impact of a ligand binding on strand migration in the SAM-I riboswitch. PLoS Comput Biol (2013) 0.81
A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions. J Mol Model (2014) 0.81
Coarse-grained prediction of RNA loop structures. PLoS One (2012) 0.80
Protein-RNA complexes and efficient automatic docking: expanding RosettaDock possibilities. PLoS One (2014) 0.79
Evaluating mixture models for building RNA knowledge-based potentials. J Bioinform Comput Biol (2012) 0.79
Optimization of an AMBER force field for the artificial nucleic acid, LNA, and benchmarking with NMR of L(CAAU). J Phys Chem B (2014) 0.79
Novel conformation of an RNA structural switch. Biochemistry (2012) 0.78
WebRASP: a server for computing energy scores to assess the accuracy and stability of RNA 3D structures. Bioinformatics (2013) 0.77
Information-theoretic uncertainty of SCFG-modeled folding space of the non-coding RNA. J Theor Biol (2012) 0.77
3dRNAscore: a distance and torsion angle dependent evaluation function of 3D RNA structures. Nucleic Acids Res (2015) 0.76
Capturing RNA Folding Free Energy with Coarse-Grained Molecular Dynamics Simulations. Sci Rep (2017) 0.75
GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies. PLoS One (2015) 0.75
Basic local alignment search tool. J Mol Biol (1990) 659.07
Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res (2003) 77.89
The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res (2006) 13.44
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci (2002) 7.40
How RNA folds. J Mol Biol (1999) 6.14
Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J Mol Biol (1990) 6.08
RNA backbone is rotameric. Proc Natl Acad Sci U S A (2003) 5.93
The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature (2008) 5.67
Theory and applications of the generalized Born solvation model in macromolecular simulations. Biopolymers (2001) 4.68
Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme. J Mol Biol (1985) 4.56
Hierarchy and dynamics of RNA folding. Annu Rev Biophys Biomol Struct (1997) 3.95
An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J Mol Biol (1998) 3.90
Automated de novo prediction of native-like RNA tertiary structures. Proc Natl Acad Sci U S A (2007) 3.87
Atomic accuracy in predicting and designing noncanonical RNA structure. Nat Methods (2010) 3.07
PDB file parser and structure class implemented in Python. Bioinformatics (2003) 2.93
A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins (2001) 2.71
Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. RNA (2009) 2.63
Bridging the gap in RNA structure prediction. Curr Opin Struct Biol (2007) 2.41
Near-native structure refinement using in vacuo energy minimization. Proc Natl Acad Sci U S A (2007) 2.12
iFoldRNA: three-dimensional RNA structure prediction and folding. Bioinformatics (2008) 2.03
An improved protein decoy set for testing energy functions for protein structure prediction. Proteins (2003) 1.94
Frequency and isostericity of RNA base pairs. Nucleic Acids Res (2009) 1.88
RNABase: an annotated database of RNA structures. Nucleic Acids Res (2003) 1.74
Revolutions in RNA secondary structure prediction. J Mol Biol (2006) 1.74
An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state. Protein Sci (2004) 1.74
New Monte Carlo algorithms for protein folding. Curr Opin Struct Biol (1999) 1.63
Classification and energetics of the base-phosphate interactions in RNA. Nucleic Acids Res (2009) 1.43
Parameters of monovalent ions in the AMBER-99 forcefield: assessment of inaccuracies and proposed improvements. J Phys Chem B (2007) 1.31
Solvent dramatically affects protein structure refinement. Proc Natl Acad Sci U S A (2008) 1.29
Turning limited experimental information into 3D models of RNA. RNA (2010) 1.27
RNA secondary structure analysis using the Vienna RNA package. Curr Protoc Bioinformatics (2009) 1.26
Using a hydrophobic contact potential to evaluate native and near-native folds generated by molecular dynamics simulations. J Mol Biol (1996) 1.26
Beyond Mfold: recent advances in RNA bioinformatics. J Biotechnol (2006) 1.23
Extracting stacking interaction parameters for RNA from the data set of native structures. J Mol Biol (2005) 1.22
A probabilistic model of RNA conformational space. PLoS Comput Biol (2009) 1.22
Describing RNA structure by libraries of clustered nucleotide doublets. J Mol Biol (2005) 1.18
Consistent refinement of submitted models at CASP using a knowledge-based potential. Proteins (2010) 1.00
Artefacts and biases affecting the evaluation of scoring functions on decoy sets for protein structure prediction. Bioinformatics (2009) 0.88
The ASTRAL Compendium in 2004. Nucleic Acids Res (2004) 10.03
Super-resolution biomolecular crystallography with low-resolution data. Nature (2010) 6.14
Within the twilight zone: a sensitive profile-profile comparison tool based on information theory. J Mol Biol (2002) 4.99
ASTRAL compendium enhancements. Nucleic Acids Res (2002) 4.43
Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures. J Mol Biol (2005) 4.02
Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution. Structure (2007) 3.16
Hydrophobic collapse in multidomain protein folding. Science (2004) 2.94
Observation of a dewetting transition in the collapse of the melittin tetramer. Nature (2005) 2.93
Mechanism of folding chamber closure in a group II chaperonin. Nature (2010) 2.85
Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution. Science (2009) 2.68
Using generalized ensemble simulations and Markov state models to identify conformational states. Methods (2009) 2.60
Near-native structure refinement using in vacuo energy minimization. Proc Natl Acad Sci U S A (2007) 2.12
Outcome of a workshop on applications of protein models in biomedical research. Structure (2009) 2.05
Small libraries of protein fragments model native protein structures accurately. J Mol Biol (2002) 1.87
Cryo-EM structure of a group II chaperonin in the prehydrolysis ATP-bound state leading to lid closure. Structure (2011) 1.71
Architecture of an RNA polymerase II transcription pre-initiation complex. Science (2013) 1.52
Simulating protein evolution in sequence and structure space. Curr Opin Struct Biol (2004) 1.50
Dynamic charge interactions create surprising rigidity in the ER/K alpha-helical protein motif. Proc Natl Acad Sci U S A (2008) 1.50
Differentiation of the roles of sulfide oxidase and rhodanese in the detoxification of sulfide by the colonic mucosa. Dig Dis Sci (2007) 1.49
A novel approach to decoy set generation: designing a physical energy function having local minima with native structure characteristics. J Mol Biol (2003) 1.46
Protein topology and stability define the space of allowed sequences. Proc Natl Acad Sci U S A (2002) 1.46
Structural insight into RNA hairpin folding intermediates. J Am Chem Soc (2008) 1.39
X-ray structure and mechanism of RNA polymerase II stalled at an antineoplastic monofunctional platinum-DNA adduct. Proc Natl Acad Sci U S A (2010) 1.39
A comprehensive analysis of 40 blind protein structure predictions. BMC Struct Biol (2002) 1.37
Subunit order of eukaryotic TRiC/CCT chaperonin by cross-linking, mass spectrometry, and combinatorial homology modeling. Proc Natl Acad Sci U S A (2012) 1.36
A role for both conformational selection and induced fit in ligand binding by the LAO protein. PLoS Comput Biol (2011) 1.35
A major role for carbon monoxide as an endogenous hyperpolarizing factor in the gastrointestinal tract. Proc Natl Acad Sci U S A (2003) 1.35
Solvent dramatically affects protein structure refinement. Proc Natl Acad Sci U S A (2008) 1.29
KoBaMIN: a knowledge-based minimization web server for protein structure refinement. Nucleic Acids Res (2012) 1.25
Mixing and matching detergents for membrane protein NMR structure determination. J Am Chem Soc (2009) 1.24
The predicted structure of the headpiece of the Huntingtin protein and its implications on Huntingtin aggregation. J Mol Biol (2009) 1.24
Diffusion of nucleoside triphosphates and role of the entry site to the RNA polymerase II active center. Proc Natl Acad Sci U S A (2004) 1.23
Nanoscale dewetting transition in protein complex folding. J Phys Chem B (2007) 1.22
Dynamics of pyrophosphate ion release and its coupled trigger loop motion from closed to open state in RNA polymerase II. J Am Chem Soc (2012) 1.20
Hydrophobic aided replica exchange: an efficient algorithm for protein folding in explicit solvent. J Phys Chem B (2006) 1.20
An atomic environment potential for use in protein structure prediction. J Mol Biol (2005) 1.19
Describing RNA structure by libraries of clustered nucleotide doublets. J Mol Biol (2005) 1.18
RNA polymerase II trigger loop residues stabilize and position the incoming nucleotide triphosphate in transcription. Proc Natl Acad Sci U S A (2010) 1.17
Improved protein structure selection using decoy-dependent discriminatory functions. BMC Struct Biol (2004) 1.15
Nonpolar solutes enhance water structure within hydration shells while reducing interactions between them. Proc Natl Acad Sci U S A (2005) 1.14
Initiation complex structure and promoter proofreading. Science (2011) 1.13
Dissecting electrostatic screening, specific ion binding, and ligand binding in an energetic model for glycine riboswitch folding. RNA (2010) 1.13
Symmetry-free cryo-EM structures of the chaperonin TRiC along its ATPase-driven conformational cycle. EMBO J (2011) 1.12
Evidence of turn and salt bridge contributions to beta-hairpin stability: MD simulations of C-terminal fragment from the B1 domain of protein G. Biophys Chem (2002) 1.12
Topological methods for exploring low-density states in biomolecular folding pathways. J Chem Phys (2009) 1.10
Funnel-like organization in sequence space determines the distributions of protein stability and folding rate preferred by evolution. Proteins (2004) 1.09
Dewetting transitions in protein cavities. Proteins (2010) 1.08
Improving the accuracy of macromolecular structure refinement at 7 Å resolution. Structure (2012) 1.06
Network models for molecular kinetics and their initial applications to human health. Cell Res (2010) 1.06
Sequence variations within protein families are linearly related to structural variations. J Mol Biol (2002) 1.06
Probing protein fold space with a simplified model. J Mol Biol (2007) 1.03
Funnel sculpting for in silico assembly of secondary structure elements of proteins. Proc Natl Acad Sci U S A (2003) 1.02
Modeling and design by hierarchical natural moves. Proc Natl Acad Sci U S A (2012) 1.02
Lactose intolerance and health. Evid Rep Technol Assess (Full Rep) (2010) 1.01
Consistent refinement of submitted models at CASP using a knowledge-based potential. Proteins (2010) 1.00
Roles of mutation and recombination in the evolution of protein thermodynamics. Proc Natl Acad Sci U S A (2002) 1.00
Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum. Acta Crystallogr D Biol Crystallogr (2012) 1.00
Conformational optimization with natural degrees of freedom: a novel stochastic chain closure algorithm. J Comput Biol (2010) 0.99
Can morphing methods predict intermediate structures? J Mol Biol (2008) 0.99
Clustering to identify RNA conformations constrained by secondary structure. Proc Natl Acad Sci U S A (2011) 0.98
Modeling nucleic acids. Curr Opin Struct Biol (2012) 0.98
Influence of mulberry leaf extract on the blood glucose and breath hydrogen response to ingestion of 75 g sucrose by type 2 diabetic and control subjects. Diabetes Care (2007) 0.98
Dynamics of water confined in the interdomain region of a multidomain protein. J Phys Chem B (2006) 0.97
Improved recognition of native-like protein structures using a family of designed sequences. Proc Natl Acad Sci U S A (2002) 0.97
Dynamics of an intrinsically disordered protein reveal metastable conformations that potentially seed aggregation. J Am Chem Soc (2013) 0.96
Impact of injury location and severity on posttraumatic epilepsy in the rat: role of frontal neocortex. Cereb Cortex (2010) 0.93
Generalized ensemble methods for de novo structure prediction. Proc Natl Acad Sci U S A (2009) 0.93
Chaotic motifs in gene regulatory networks. PLoS One (2012) 0.93
The crystal structures of the eukaryotic chaperonin CCT reveal its functional partitioning. Structure (2013) 0.93
Evolutionarily consistent families in SCOP: sequence, structure and function. BMC Struct Biol (2012) 0.92
Simulating the T-jump-triggered unfolding dynamics of trpzip2 peptide and its time-resolved IR and two-dimensional IR signals using the Markov state model approach. J Phys Chem B (2011) 0.91
Multiscale natural moves refine macromolecules using single-particle electron microscopy projection images. Proc Natl Acad Sci U S A (2012) 0.91
Inhibition mechanism of the acetylcholine receptor by alpha-neurotoxins as revealed by normal-mode dynamics. Biochemistry (2008) 0.90
MOTIF-EM: an automated computational tool for identifying conserved regions in CryoEM structures. Bioinformatics (2010) 0.90
Design of an optimal Chebyshev-expanded discrimination function for globular proteins. Protein Sci (2002) 0.90
A two-state model for the dynamics of the pyrophosphate ion release in bacterial RNA polymerase. PLoS Comput Biol (2013) 0.90
On the universe of protein folds. Annu Rev Biophys (2013) 0.89
Spatial regulation and the rate of signal transduction activation. PLoS Comput Biol (2006) 0.88
WeFold: a coopetition for protein structure prediction. Proteins (2014) 0.88
Protein segment finder: an online search engine for segment motifs in the PDB. Nucleic Acids Res (2008) 0.88
In vitro selection of mutant HDM2 resistant to Nutlin inhibition. PLoS One (2013) 0.87
Comparative modeling and protein-like features of hydrophobic-polar models on a two-dimensional lattice. Proteins (2012) 0.87
A tetraphenylethylene core-based 3D structure small molecular acceptor enabling efficient non-fullerene organic solar cells. Adv Mater (2014) 0.86
Monitoring and inhibition of insulin fibrillation by a small organic fluorogen with aggregation-induced emission characteristics. J Am Chem Soc (2012) 0.86
Electrostatics of nucleic acid folding under conformational constraint. J Am Chem Soc (2012) 0.85
How hydrophobic buckminsterfullerene affects surrounding water structure. J Phys Chem B (2008) 0.85
Multiscale modeling of macromolecular biosystems. Brief Bioinform (2012) 0.84
Insights into the intra-ring subunit order of TRiC/CCT: a structural and evolutionary analysis. Pac Symp Biocomput (2010) 0.83
Multimodality treatment of complex unruptured cavernous and paraclinoid aneurysms. Neurosurgery (2014) 0.83
Bowel problems, self-care practices, and information needs of colorectal cancer survivors at 6 to 24 months after sphincter-saving surgery. Cancer Nurs (2008) 0.83
Hierarchical Nyström methods for constructing Markov state models for conformational dynamics. J Chem Phys (2013) 0.83
Training-free atomistic prediction of nucleosome occupancy. Proc Natl Acad Sci U S A (2014) 0.83
A fast parallel clustering algorithm for molecular simulation trajectories. J Comput Chem (2012) 0.83
Population-based screening for Lynch syndrome in Western Australia. Int J Cancer (2014) 0.81
Quantitative comparison of alternative methods for coarse-graining biological networks. J Chem Phys (2013) 0.81
Remarkable patterns of surface water ordering around polarized buckminsterfullerene. Proc Natl Acad Sci U S A (2011) 0.81
Optimized torsion-angle normal modes reproduce conformational changes more accurately than cartesian modes. Biophys J (2011) 0.81
Simulations of RNA base pairs in a nanodroplet reveal solvation-dependent stability. Proc Natl Acad Sci U S A (2007) 0.81
Normal modes of prion proteins: from native to infectious particle. Biochemistry (2011) 0.80