Published in J Chem Theory Comput on March 01, 2008
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics (2013) 11.01
Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles. J Chem Theory Comput (2012) 5.57
Current status of the AMOEBA polarizable force field. J Phys Chem B (2010) 3.06
Helical extension of the neuronal SNARE complex into the membrane. Nature (2009) 2.92
Cyanine fluorophore derivatives with enhanced photostability. Nat Methods (2011) 2.85
Performance analysis of a dual-tree algorithm for computing spatial distance histograms. VLDB J (2011) 2.68
The molecular basis for selective inhibition of unconventional mRNA splicing by an IRE1-binding small molecule. Proc Natl Acad Sci U S A (2012) 2.45
Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies. PLoS Biol (2012) 2.37
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Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways. Nat Chem (2013) 2.26
MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale. J Chem Theory Comput (2011) 2.15
OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation. J Chem Theory Comput (2012) 2.07
A two-domain elevator mechanism for sodium/proton antiport. Nature (2013) 2.05
Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum. Proc Natl Acad Sci U S A (2011) 1.96
SMOG@ctbp: simplified deployment of structure-based models in GROMACS. Nucleic Acids Res (2010) 1.95
Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways. RNA (2010) 1.91
Dielectric properties of water under extreme conditions and transport of carbonates in the deep Earth. Proc Natl Acad Sci U S A (2013) 1.89
Association of lipidome remodeling in the adipocyte membrane with acquired obesity in humans. PLoS Biol (2011) 1.89
To milliseconds and beyond: challenges in the simulation of protein folding. Curr Opin Struct Biol (2012) 1.77
Polarizable water model for the coarse-grained MARTINI force field. PLoS Comput Biol (2010) 1.76
Structure of the yeast F1Fo-ATP synthase dimer and its role in shaping the mitochondrial cristae. Proc Natl Acad Sci U S A (2012) 1.76
Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements. J Chem Theory Comput (2012) 1.68
Challenges in protein folding simulations: Timescale, representation, and analysis. Nat Phys (2010) 1.67
The energy landscape of adenylate kinase during catalysis. Nat Struct Mol Biol (2015) 1.62
Crystal structure of a eukaryotic phosphate transporter. Nature (2013) 1.60
Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis. Proc Natl Acad Sci U S A (2012) 1.57
A novel side-chain orientation dependent potential derived from random-walk reference state for protein fold selection and structure prediction. PLoS One (2010) 1.56
Proteome-wide analysis of lysine acetylation suggests its broad regulatory scope in Saccharomyces cerevisiae. Mol Cell Proteomics (2012) 1.55
Mechanistic Insight into NMDA Receptor Dysregulation by Rare Variants in the GluN2A and GluN2B Agonist Binding Domains. Am J Hum Genet (2016) 1.54
Nothing to sneeze at: a dynamic and integrative computational model of an influenza A virion. Structure (2015) 1.54
Computer-aided drug design platform using PyMOL. J Comput Aided Mol Des (2010) 1.53
Conformational changes and slow dynamics through microsecond polarized atomistic molecular simulation of an integral Kv1.2 ion channel. PLoS Comput Biol (2009) 1.51
Lipid packing drives the segregation of transmembrane helices into disordered lipid domains in model membranes. Proc Natl Acad Sci U S A (2011) 1.50
Conformational analysis of processivity clamps in solution demonstrates that tertiary structure does not correlate with protein dynamics. Structure (2014) 1.49
Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser. Nat Methods (2014) 1.49
Immune history shapes specificity of pandemic H1N1 influenza antibody responses. J Exp Med (2013) 1.47
Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering. J Chem Theory Comput (2015) 1.47
Balanced Protein-Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association. J Chem Theory Comput (2014) 1.47
Molecular determinants for nuclear import of influenza A PB2 by importin α isoforms 3 and 7. Structure (2015) 1.47
Tracking a complete voltage-sensor cycle with metal-ion bridges. Proc Natl Acad Sci U S A (2012) 1.46
The effects of threonine phosphorylation on the stability and dynamics of the central molecular switch region of 18.5-kDa myelin basic protein. PLoS One (2013) 1.46
Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant. J Chem Theory Comput (2011) 1.46
The five-to-six-coordination transition of ferric human serum heme-albumin is allosterically-modulated by ibuprofen and warfarin: a combined XAS and MD study. PLoS One (2014) 1.45
Exploring atomic resolution physiology on a femtosecond to millisecond timescale using molecular dynamics simulations. J Gen Physiol (2010) 1.44
Simple few-state models reveal hidden complexity in protein folding. Proc Natl Acad Sci U S A (2012) 1.43
Surface Density-Induced Pleating of a Lipid Monolayer Drives Nascent High-Density Lipoprotein Assembly. Structure (2015) 1.43
Accurate Prediction of Ligand Affinities for a Proton-Dependent Oligopeptide Transporter. Cell Chem Biol (2016) 1.42
An interdomain sector mediating allostery in Hsp70 molecular chaperones. Mol Syst Biol (2010) 1.42
Atomic-resolution simulations predict a transition state for vesicle fusion defined by contact of a few lipid tails. PLoS Comput Biol (2010) 1.42
Mechanistic and structural insight into the functional dichotomy between IL-2 and IL-15. Nat Immunol (2012) 1.41
Distance Histogram Computation Based on Spatiotemporal Uniformity in Scientific Data. Adv Database Technol (2012) 1.41
Sitting at the edge: how biomolecules use hydrophobicity to tune their interactions and function. J Phys Chem B (2012) 1.40
Phytochemicals perturb membranes and promiscuously alter protein function. ACS Chem Biol (2014) 1.39
Phosphatidylinositol 4,5-bisphosphate clusters act as molecular beacons for vesicle recruitment. Nat Struct Mol Biol (2013) 1.38
Structure and dynamics of the membrane-bound cytochrome P450 2C9. PLoS Comput Biol (2011) 1.37
Derivation and systematic validation of a refined all-atom force field for phosphatidylcholine lipids. J Phys Chem B (2012) 1.36
Single molecule diffusion of membrane-bound proteins: window into lipid contacts and bilayer dynamics. Biophys J (2010) 1.35
DCMS: A data analytics and management system for molecular simulation. J Big Data (2014) 1.35
Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites. Proc Natl Acad Sci U S A (2012) 1.34
Multiscaled exploration of coupled folding and binding of an intrinsically disordered molecular recognition element in measles virus nucleoprotein. Proc Natl Acad Sci U S A (2013) 1.34
Protein thermostability calculations using alchemical free energy simulations. Biophys J (2010) 1.33
Drug design for neuropathic pain regulation from traditional Chinese medicine. Sci Rep (2013) 1.30
Multivalent histone engagement by the linked tandem Tudor and PHD domains of UHRF1 is required for the epigenetic inheritance of DNA methylation. Genes Dev (2013) 1.30
Computational electrophysiology: the molecular dynamics of ion channel permeation and selectivity in atomistic detail. Biophys J (2011) 1.30
MOIL-opt: Energy-Conserving Molecular Dynamics on a GPU/CPU system. J Chem Theory Comput (2011) 1.27
Release of content through mechano-sensitive gates in pressurized liposomes. Proc Natl Acad Sci U S A (2010) 1.26
Organization, dynamics, and segregation of Ras nanoclusters in membrane domains. Proc Natl Acad Sci U S A (2012) 1.25
Allosteric pathways in imidazole glycerol phosphate synthase. Proc Natl Acad Sci U S A (2012) 1.24
Structure of the TatC core of the twin-arginine protein transport system. Nature (2012) 1.23
Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein. Science (2016) 1.23
Indolicidin binding induces thinning of a lipid bilayer. Biophys J (2014) 1.22
ReaDDy--a software for particle-based reaction-diffusion dynamics in crowded cellular environments. PLoS One (2013) 1.21
The molecular mechanism of substrate engagement and immunosuppressant inhibition of calcineurin. PLoS Biol (2013) 1.21
Dynamic allostery in the methionine repressor revealed by force distribution analysis. PLoS Comput Biol (2009) 1.21
Computational identification of a transiently open L1/S3 pocket for reactivation of mutant p53. Nat Commun (2013) 1.21
Porphyrin-phospholipid liposomes permeabilized by near-infrared light. Nat Commun (2014) 1.20
Scaling behaviour for the water transport in nanoconfined geometries. Nat Commun (2014) 1.20
Modeling aqueous solvation with semi-explicit assembly. Proc Natl Acad Sci U S A (2011) 1.20
Amphipathic lipid packing sensor motifs: probing bilayer defects with hydrophobic residues. Biophys J (2013) 1.19
MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories. Biophys J (2015) 1.19
Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics. Proc Natl Acad Sci U S A (2013) 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
Construction and validation of a homology model of the human voltage-gated proton channel hHV1. J Gen Physiol (2013) 1.17
Parallel Generalized Born Implicit Solvent Calculations with NAMD. J Chem Theory Comput (2011) 1.17
Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences. Proteins (2011) 1.16
All-atom polarizable force field for DNA based on the classical Drude oscillator model. J Comput Chem (2014) 1.16
VEGFR2 functions as an H2S-targeting receptor protein kinase with its novel Cys1045-Cys1024 disulfide bond serving as a specific molecular switch for hydrogen sulfide actions in vascular endothelial cells. Antioxid Redox Signal (2013) 1.16
Slipknotting upon native-like loop formation in a trefoil knot protein. Proc Natl Acad Sci U S A (2010) 1.15
A preformed binding interface in the unbound ensemble of an intrinsically disordered protein: evidence from molecular simulations. PLoS Comput Biol (2012) 1.15
Dynamics and dissipation in enzyme catalysis. Proc Natl Acad Sci U S A (2011) 1.15
Virus capsid dissolution studied by microsecond molecular dynamics simulations. PLoS Comput Biol (2012) 1.14
Mutational analysis of the high-affinity zinc binding site validates a refined human dopamine transporter homology model. PLoS Comput Biol (2013) 1.14
Identification of cardiolipin binding sites on cytochrome c oxidase at the entrance of proton channels. Sci Rep (2013) 1.14
Nucleotide-dependent mechanism of Get3 as elucidated from free energy calculations. Proc Natl Acad Sci U S A (2012) 1.14
Making structural sense of dimerization interfaces of delta opioid receptor homodimers. Biochemistry (2011) 1.13
Calculations of the electric fields in liquid solutions. J Phys Chem B (2013) 1.13
α-Synuclein induces both positive mean curvature and negative Gaussian curvature in membranes. J Am Chem Soc (2012) 1.13
PIP2 controls voltage-sensor movement and pore opening of Kv channels through the S4-S5 linker. Proc Natl Acad Sci U S A (2012) 1.13
N-Ras forms dimers at POPC membranes. Biophys J (2012) 1.13
Lipid clustering correlates with membrane curvature as revealed by molecular simulations of complex lipid bilayers. PLoS Comput Biol (2014) 1.13