The Simbios National Center: Systems Biology in Motion.

Simbody: multibody dynamics for biomedical research. Procedia IUTAM (2015) 1.61

Predicting RNA structure by multiple template homology modeling. Pac Symp Biocomput (2010) 1.12

Subject-specific, multiscale simulation of electrophysiology: a software pipeline for image-based models and application examples. Philos Trans A Math Phys Eng Sci (2009) 1.12

Minimal formulation of joint motion for biomechanisms. Nonlinear Dyn (2010) 1.01

Simbios: an NIH national center for physics-based simulation of biological structures. J Am Med Inform Assoc (2011) 0.94

Characterization of the transport topology in patient-specific abdominal aortic aneurysm models. Phys Fluids (1994) (2012) 0.91

Potential fluid mechanic pathways of platelet activation. Biomech Model Mechanobiol (2012) 0.89

A longitudinal comparison of hemodynamics and intraluminal thrombus deposition in abdominal aortic aneurysms. Am J Physiol Heart Circ Physiol (2014) 0.87

A non-discrete method for computation of residence time in fluid mechanics simulations. Phys Fluids (1994) (2013) 0.85

Lagrangian analysis of hemodynamics data from FSI simulation. Int J Numer Method Biomed Eng (2012) 0.84

Strategies for articulated multibody-based adaptive coarse grain simulation of RNA. Methods Enzymol (2011) 0.82

Effect of exercise on patient specific abdominal aortic aneurysm flow topology and mixing. Int J Numer Method Biomed Eng (2013) 0.81

Distribution of aerosolized particles in healthy and emphysematous rat lungs: comparison between experimental and numerical studies. J Biomech (2015) 0.80

In Vitro Validation of Patient-Specific Hemodynamic Simulations in Coronary Aneurysms Caused by Kawasaki Disease. Cardiovasc Eng Technol (2014) 0.78

Simulation based planning of surgical interventions in pediatric cardiology. Phys Fluids (1994) (2013) 0.78

Toward large-scale computational fluid-solid-growth models of intracranial aneurysms. Yale J Biol Med (2012) 0.76

Simulations reveal adverse hemodynamics in patients with multiple systemic to pulmonary shunts. J Biomech Eng (2015) 0.75

The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science (2000) 28.25

Structure of the 30S ribosomal subunit. Nature (2000) 23.11

Crystal structure of the ribosome at 5.5 A resolution. Science (2001) 18.21

Crystal structure of a group I ribozyme domain: principles of RNA packing. Science (1996) 13.99

Molecular dynamics simulations of biomolecules. Nat Struct Biol (2002) 7.68

OpenSim: open-source software to create and analyze dynamic simulations of movement. IEEE Trans Biomed Eng (2007) 6.50

Self-splicing of group I introns. Annu Rev Biochem (1990) 6.36

Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics. Chem Rev (1999) 6.22

Absolute comparison of simulated and experimental protein-folding dynamics. Nature (2002) 5.68

An interactive graphics-based model of the lower extremity to study orthopaedic surgical procedures. IEEE Trans Biomed Eng (1990) 5.65

SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments. RNA (2005) 3.95

Riboswitches as versatile gene control elements. Curr Opin Struct Biol (2005) 3.83

COMPUTING: Screen Savers of the World Unite! Science (2000) 3.54

Three conformational states of scallop myosin S1. Proc Natl Acad Sci U S A (2000) 3.06

A preorganized active site in the crystal structure of the Tetrahymena ribozyme. Science (1998) 3.01

Dynamic optimization of human walking. J Biomech Eng (2001) 2.96

Internal coordinates for molecular dynamics and minimization in structure determination and refinement. J Magn Reson (2001) 2.75

Lead discovery using molecular docking. Curr Opin Chem Biol (2002) 2.62

RNA and protein folding: common themes and variations. Biochemistry (2005) 2.47

Generating dynamic simulations of movement using computed muscle control. J Biomech (2003) 2.46

A graphics-based software system to develop and analyze models of musculoskeletal structures. Comput Biol Med (1995) 2.18

Molecular dynamics simulations. Curr Opin Struct Biol (2002) 1.93

Probing the folding landscape of the Tetrahymena ribozyme: commitment to form the native conformation is late in the folding pathway. J Mol Biol (2001) 1.80

Muscle coordination of movement: a perspective. J Biomech (1993) 1.66

Whole-cell simulation: a grand challenge of the 21st century. Trends Biotechnol (2001) 1.56

Rapid calculation of polar molecular surface area and its application to the prediction of transport phenomena. 1. Prediction of intestinal absorption. J Pharm Sci (1999) 1.45

Local kinetic measures of macromolecular structure reveal partitioning among multiple parallel pathways from the earliest steps in the folding of a large RNA molecule. J Mol Biol (2006) 1.38

Generalized coarse-grained model based on point multipole and Gay-Berne potentials. J Chem Phys (2006) 1.08

Empirical modifications to the Amber/OPLS potential for predicting the solution conformations of cyclic peptides by vacuum calculations. Fold Des (1998) 0.85

A microstructurally informed model for the mechanical response of three-dimensional actin networks. Comput Methods Biomech Biomed Engin (2008) 0.81

Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell (2012) 12.32

Clinical assessment incorporating a personal genome. Lancet (2010) 10.18

The chemical genomic portrait of yeast: uncovering a phenotype for all genes. Science (2008) 8.52

The incidentalome: a threat to genomic medicine. JAMA (2006) 7.24

Genetics. Genomic research and human subject privacy. Science (2004) 6.56

PharmGKB: the Pharmacogenetics Knowledge Base. Nucleic Acids Res (2002) 6.40

A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proc Natl Acad Sci U S A (2003) 6.19

Absolute comparison of simulated and experimental protein-folding dynamics. Nature (2002) 5.68

Accelerating molecular dynamic simulation on graphics processing units. J Comput Chem (2009) 4.58

Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics. J Chem Phys (2007) 4.52

Random-coil behavior and the dimensions of chemically unfolded proteins. Proc Natl Acad Sci U S A (2004) 4.44

Exploring the helix-coil transition via all-atom equilibrium ensemble simulations. Biophys J (2005) 4.26

From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource. Biomark Med (2011) 4.05

Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO). Bioinformatics (2003) 3.97

SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments. RNA (2005) 3.95

Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature. Genome Res (2002) 3.77

Nonparametric methods for identifying differentially expressed genes in microarray data. Bioinformatics (2002) 3.65

Health-information altruists--a potentially critical resource. N Engl J Med (2005) 3.61

The RNA Ontology Consortium: an open invitation to the RNA community. RNA (2006) 3.60

Multiplexed-replica exchange molecular dynamics method for protein folding simulation. Biophys J (2003) 3.35

Creating an online dictionary of abbreviations from MEDLINE. J Am Med Inform Assoc (2002) 3.32

A model of the upper extremity for simulating musculoskeletal surgery and analyzing neuromuscular control. Ann Biomed Eng (2005) 3.21

Genetic variants associated with warfarin dose in African-American individuals: a genome-wide association study. Lancet (2013) 3.21

Phased whole-genome genetic risk in a family quartet using a major allele reference sequence. PLoS Genet (2011) 3.20

Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39). J Am Chem Soc (2010) 3.18

Current status of the AMOEBA polarizable force field. J Phys Chem B (2010) 3.06

Data-driven prediction of drug effects and interactions. Sci Transl Med (2012) 2.93

Challenges in the clinical application of whole-genome sequencing. Lancet (2010) 2.92

Eukaryotic regulatory element conservation analysis and identification using comparative genomics. Genome Res (2004) 2.84

Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece. J Mol Biol (2007) 2.77

Solvation free energies of amino acid side chain analogs for common molecular mechanics water models. J Chem Phys (2005) 2.76

Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing. J Mol Biol (2002) 2.73

PharmGKB: a logical home for knowledge relating genotype to drug response phenotype. Nat Genet (2007) 2.65

Progress and challenges in the automated construction of Markov state models for full protein systems. J Chem Phys (2009) 2.64

Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. RNA (2009) 2.63

Using generalized ensemble simulations and Markov state models to identify conformational states. Methods (2009) 2.60

Minimally invasive high-speed imaging of sarcomere contractile dynamics in mice and humans. Nature (2008) 2.56

A novel signal detection algorithm for identifying hidden drug-drug interactions in adverse event reports. J Am Med Inform Assoc (2011) 2.53

Clinical implementation of pharmacogenomics: overcoming genetic exceptionalism. Lancet Oncol (2010) 2.52

A model of the lower limb for analysis of human movement. Ann Biomed Eng (2009) 2.50

Generating dynamic simulations of movement using computed muscle control. J Biomech (2003) 2.46

The pharmacogenetics and pharmacogenomics knowledge base: accentuating the knowledge. Nucleic Acids Res (2007) 2.45

Time-resolved three-dimensional phase-contrast MRI. J Magn Reson Imaging (2003) 2.43

The Pharmacogenomics Research Network Translational Pharmacogenetics Program: overcoming challenges of real-world implementation. Clin Pharmacol Ther (2013) 2.39

Muscles that support the body also modulate forward progression during walking. J Biomech (2005) 2.35

Electric fields at the active site of an enzyme: direct comparison of experiment with theory. Science (2006) 2.32

Alchemical free energy methods for drug discovery: progress and challenges. Curr Opin Struct Biol (2011) 2.31

Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration. J Chem Phys (2005) 2.31

Equilibrium free energies from nonequilibrium measurements using maximum-likelihood methods. Phys Rev Lett (2003) 2.30

Using path sampling to build better Markovian state models: predicting the folding rate and mechanism of a tryptophan zipper beta hairpin. J Chem Phys (2004) 2.30

Bioinformatics challenges for personalized medicine. Bioinformatics (2011) 2.28

Protein folded states are kinetic hubs. Proc Natl Acad Sci U S A (2010) 2.27

Predicting small-molecule solvation free energies: an informal blind test for computational chemistry. J Med Chem (2008) 2.27

The Trp cage: folding kinetics and unfolded state topology via molecular dynamics simulations. J Am Chem Soc (2002) 2.26

Time to organize the bioinformatics resourceome. PLoS Comput Biol (2005) 2.25

MScanner: a classifier for retrieving Medline citations. BMC Bioinformatics (2008) 2.24

Native-like mean structure in the unfolded ensemble of small proteins. J Mol Biol (2002) 2.23

Using binning to maintain confidentiality of medical data. Proc AMIA Symp (2002) 2.23

Using massively parallel simulation and Markovian models to study protein folding: examining the dynamics of the villin headpiece. J Chem Phys (2006) 2.22

Web-scale pharmacovigilance: listening to signals from the crowd. J Am Med Inform Assoc (2013) 2.19

Using text to build semantic networks for pharmacogenomics. J Biomed Inform (2010) 2.19

MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale. J Chem Theory Comput (2011) 2.15

Pharmspresso: a text mining tool for extraction of pharmacogenomic concepts and relationships from full text. BMC Bioinformatics (2009) 2.15

PharmGKB: understanding the effects of individual genetic variants. Drug Metab Rev (2008) 2.09

Exploiting a natural conformational switch to engineer an interleukin-2 'superkine'. Nature (2012) 2.08

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation. J Chem Theory Comput (2012) 2.07

GAPSCORE: finding gene and protein names one word at a time. Bioinformatics (2004) 2.05

How well can simulation predict protein folding kinetics and thermodynamics? Annu Rev Biophys Biomol Struct (2005) 1.98

Pharmacogenomics: challenges and opportunities. Ann Intern Med (2006) 1.96

Simulations of the role of water in the protein-folding mechanism. Proc Natl Acad Sci U S A (2004) 1.95

Atomistic folding simulations of the five-helix bundle protein λ(6−85). J Am Chem Soc (2011) 1.94

Muscle contributions to support and progression over a range of walking speeds. J Biomech (2008) 1.94

Computational analysis of Plasmodium falciparum metabolism: organizing genomic information to facilitate drug discovery. Genome Res (2004) 1.92

Pharmacogenomics and bioinformatics: PharmGKB. Pharmacogenomics (2010) 1.91

A 3D model of muscle reveals the causes of nonuniform strains in the biceps brachii. J Biomech (2005) 1.90

Grand challenge competition to predict in vivo knee loads. J Orthop Res (2011) 1.90

Muscle contributions to propulsion and support during running. J Biomech (2010) 1.89

Recent progress in automatically extracting information from the pharmacogenomic literature. Pharmacogenomics (2010) 1.88

Direct calculation of the binding free energies of FKBP ligands. J Chem Phys (2005) 1.88

Automating data acquisition into ontologies from pharmacogenetics relational data sources using declarative object definitions and XML. Pac Symp Biocomput (2002) 1.81

PharmGKB: the Pharmacogenomics Knowledge Base. Methods Mol Biol (2013) 1.81

PharmGKB: the pharmacogenetics and pharmacogenomics knowledge base. Methods Mol Biol (2005) 1.80

High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis. Nucleic Acids Res (2008) 1.78

To milliseconds and beyond: challenges in the simulation of protein folding. Curr Opin Struct Biol (2012) 1.77

Muscular contributions to hip and knee extension during the single limb stance phase of normal gait: a framework for investigating the causes of crouch gait. J Biomech (2004) 1.74

Using text analysis to identify functionally coherent gene groups. Genome Res (2002) 1.71

Error analysis and efficient sampling in Markovian state models for molecular dynamics. J Chem Phys (2005) 1.70

Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements. J Chem Theory Comput (2012) 1.68

The FEATURE framework for protein function annotation: modeling new functions, improving performance, and extending to novel applications. BMC Genomics (2008) 1.64

Evaluation of a novel Y-shaped extracardiac Fontan baffle using computational fluid dynamics. J Thorac Cardiovasc Surg (2009) 1.62

Quantification of hemodynamics in abdominal aortic aneurysms during rest and exercise using magnetic resonance imaging and computational fluid dynamics. Ann Biomed Eng (2010) 1.61

Finding haplotype tagging SNPs by use of principal components analysis. Am J Hum Genet (2004) 1.61

Six-week gait retraining program reduces knee adduction moment, reduces pain, and improves function for individuals with medial compartment knee osteoarthritis. J Orthop Res (2013) 1.61

The Fip35 WW domain folds with structural and mechanistic heterogeneity in molecular dynamics simulations. Biophys J (2009) 1.58

Allometric scaling of wall shear stress from mice to humans: quantification using cine phase-contrast MRI and computational fluid dynamics. Am J Physiol Heart Circ Physiol (2006) 1.57

Nonuniform shortening in the biceps brachii during elbow flexion. J Appl Physiol (1985) (2002) 1.57

The three-dimensional micro- and nanostructure of the aortic medial lamellar unit measured using 3D confocal and electron microscopy imaging. Matrix Biol (2007) 1.56

Efficient nonbonded interactions for molecular dynamics on a graphics processing unit. J Comput Chem (2010) 1.55

Rapid equilibrium sampling initiated from nonequilibrium data. Proc Natl Acad Sci U S A (2009) 1.54

MutDB: annotating human variation with functionally relevant data. Bioinformatics (2003) 1.54