| scholarly article | Q13442814 |
| P819 | ADS bibcode | 2016NatCo...712965H |
| P356 | DOI | 10.1038/NCOMMS12965 |
| P2888 | exact match | https://scigraph.springernature.com/pub.10.1038/ncomms12965 |
| P932 | PMC publication ID | 5477488 |
| P698 | PubMed publication ID | 27708258 |
| P50 | author | Kathryn M. Hart | Q55091069 |
| P2093 | author name string | Michael L Gross | |
| Gregory R Bowman | |||
| Supratik Dutta | |||
| Chris M W Ho | |||
| P2860 | cites work | Confidence limits, error bars and method comparison in molecular modeling. Part 1: the calculation of confidence intervals | Q24289469 |
| Updated functional classification of beta-lactamases | Q24644798 | ||
| Comparison of simple potential functions for simulating liquid water | Q26778447 | ||
| Markov state models of biomolecular conformational dynamics | Q26827934 | ||
| The ensemble nature of allostery | Q26862004 | ||
| An improved relaxed complex scheme for receptor flexibility in computer-aided drug design | Q36838120 | ||
| Using generalized ensemble simulations and Markov state models to identify conformational states | Q37366740 | ||
| Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways | Q37582165 | ||
| Natural evolution of TEM-1 β-lactamase: experimental reconstruction and clinical relevance | Q37735903 | ||
| MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale | Q39373045 | ||
| Backbone dynamics of TEM-1 determined by NMR: evidence for a highly ordered protein | Q40287526 | ||
| Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models | Q40776037 | ||
| Multiple substitutions at position 104 of beta-lactamase TEM-1: assessing the role of this residue in substrate specificity. | Q41850654 | ||
| Negative Epistasis and Evolvability in TEM-1 β-Lactamase--The Thin Line between an Enzyme's Conformational Freedom and Disorder | Q42686900 | ||
| Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search | Q46358770 | ||
| Evolution of conformational dynamics determines the conversion of a promiscuous generalist into a specialist enzyme. | Q47595845 | ||
| Evolvability as a function of purifying selection in TEM-1 β-lactamase. | Q50438672 | ||
| P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation. | Q51897570 | ||
| Investigation of the folding pathway of the TEM-1 beta-lactamase. | Q52340739 | ||
| Ensemble-based docking using biased molecular dynamics. | Q53145450 | ||
| Mass spectral kinetic study of acylation and deacylation during the hydrolysis of penicillins and cefotaxime by beta-lactamase TEM-1 and the G238S mutant. | Q54603776 | ||
| TEM beta-lactamase mutants hydrolysing third-generation cephalosporins. A kinetic and molecular modelling analysis. | Q54622202 | ||
| Substitution of lysine at position 104 or 240 of TEM-1pTZ18R beta-lactamase enhances the effect of serine-164 substitution on hydrolysis or affinity for cephalosporins and the monobactam aztreonam. | Q54698245 | ||
| The effect of high-frequency random mutagenesis on in vitro protein evolution: a study on TEM-1 beta-lactamase | Q56902347 | ||
| Molecular dynamics with coupling to an external bath | Q57569060 | ||
| Scoring noncovalent protein-ligand interactions: a continuous differentiable function tuned to compute binding affinities | Q71851460 | ||
| The role of residue 238 of TEM-1 beta-lactamase in the hydrolysis of extended-spectrum antibiotics | Q77359780 | ||
| Polymorphic transitions in single crystals: A new molecular dynamics method | Q97681190 | ||
| An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation | Q104529437 | ||
| A smooth particle mesh Ewald method | Q107213707 | ||
| Predicting the emergence of antibiotic resistance by directed evolution and structural analysis | Q27630116 | ||
| Molecular structure of the acyl-enzyme intermediate in beta-lactam hydrolysis at 1.7 A resolution | Q27642162 | ||
| Hidden alternative structures of proline isomerase essential for catalysis | Q27658415 | ||
| Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery | Q27684410 | ||
| Crystal structure of Escherichia coli TEM1 beta-lactamase at 1.8 A resolution | Q27731984 | ||
| GROMACS: fast, flexible, and free | Q27860998 | ||
| A role for both conformational selection and induced fit in ligand binding by the LAO protein | Q28478319 | ||
| A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations | Q29547632 | ||
| Darwinian evolution can follow only very few mutational paths to fitter proteins | Q29616042 | ||
| Canonical sampling through velocity rescaling | Q29616131 | ||
| Intrinsic dynamics of an enzyme underlies catalysis | Q29616406 | ||
| The dynamic energy landscape of dihydrofolate reductase catalysis | Q29616409 | ||
| Dynamic personalities of proteins | Q29616723 | ||
| Laser flash photolysis of hydrogen peroxide to oxidize protein solvent-accessible residues on the microsecond timescale. | Q30351743 | ||
| Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking. | Q30357936 | ||
| Comparative Protein Structure Modeling Using MODELLER | Q30366550 | ||
| Protein dynamism and evolvability. | Q30376087 | ||
| Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations. | Q30501558 | ||
| Rapid equilibrium sampling initiated from nonequilibrium data | Q33508733 | ||
| Fast photochemical oxidation of protein footprints faster than protein unfolding | Q33546010 | ||
| Extensive conformational heterogeneity within protein cores | Q33784732 | ||
| Secretion cloning vectors in Escherichia coli | Q33940005 | ||
| Network models for molecular kinetics and their initial applications to human health | Q34112333 | ||
| Predicting evolution by in vitro evolution requires determining evolutionary pathways | Q34112966 | ||
| Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites | Q34323850 | ||
| Fast photochemical oxidation of proteins and mass spectrometry follow submillisecond protein folding at the amino-acid level | Q34449755 | ||
| A secondary drug resistance mutation of TEM-1 beta-lactamase that suppresses misfolding and aggregation | Q34594475 | ||
| Discovery of multiple hidden allosteric sites by combining Markov state models and experiments | Q35156860 | ||
| Mass spectrometry-based protein footprinting characterizes the structures of oligomeric apolipoprotein E2, E3, and E4. | Q35226230 | ||
| Systematic mutagenesis of the active site omega loop of TEM-1 beta-lactamase | Q35604377 | ||
| Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement | Q35693509 | ||
| MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories. | Q35816082 | ||
| PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models. | Q35843343 | ||
| Allostery through the computational microscope: cAMP activation of a canonical signalling domain | Q35858462 | ||
| A natural polymorphism in beta-lactamase is a global suppressor | Q36560876 | ||
| The dark energy of proteins comes to light: conformational entropy and its role in protein function revealed by NMR relaxation | Q36609458 | ||
| P275 | copyright license | Creative Commons Attribution 4.0 International | Q20007257 |
| P6216 | copyright status | copyrighted | Q50423863 |
| P407 | language of work or name | English | Q1860 |
| P921 | main subject | antibiotic resistance | Q380775 |
| P304 | page(s) | 12965 | |
| P577 | publication date | 2016-10-06 | |
| P1433 | published in | Nature Communications | Q573880 |
| P1476 | title | Modelling proteins' hidden conformations to predict antibiotic resistance | |
| P478 | volume | 7 |
| Q90015973 | A Fast Photochemical Oxidation of Proteins (FPOP) platform for free-radical reactions: the carbonate radical anion with peptides and proteins |
| Q90568175 | Advanced Methods for Accessing Protein Shape-Shifting Present New Therapeutic Opportunities |
| Q98178435 | Allosteric Regulation at the Crossroads of New Technologies: Multiscale Modeling, Networks, and Machine Learning |
| Q47142673 | Bladder-cancer-associated mutations in RXRA activate peroxisome proliferator-activated receptors to drive urothelial proliferation. |
| Q57797778 | Choice of Adaptive Sampling Strategy Impacts State Discovery, Transition Probabilities, and the Apparent Mechanism of Conformational Changes |
| Q97426501 | Citizen Scientists Create an Exascale Computer to Combat COVID-19 |
| Q38674854 | Combining experimental and simulation data of molecular processes via augmented Markov models. |
| Q64926659 | Conformational dynamics and enzyme evolution. |
| Q58465760 | Defining the architecture of KPC-2 Carbapenemase: identifying allosteric networks to fight antibiotics resistance |
| Q36389619 | Designing small molecules to target cryptic pockets yields both positive and negative allosteric modulators |
| Q90182025 | Dynamics Rationalize Proteolytic Susceptibility of the Major Birch Pollen Allergen Bet v 1 |
| Q52688152 | Electron Cryo-microscopy Structure of Ebola Virus Nucleoprotein Reveals a Mechanism for Nucleocapsid-like Assembly. |
| Q89500394 | Hierarchical Markov State Model Building to Describe Molecular Processes |
| Q88815093 | Implementing fast photochemical oxidation of proteins (FPOP) as a footprinting approach to solve diverse problems in structural biology |
| Q89803412 | Inhibition of striatal-enriched protein tyrosine phosphatase by targeting computationally revealed cryptic pockets |
| Q89510669 | Integrated Computational Approaches and Tools forAllosteric Drug Discovery |
| Q90061707 | Investigating Cryptic Binding Sites by Molecular Dynamics Simulations |
| Q49944123 | Mass Spectrometry-Based Fast Photochemical Oxidation of Proteins (FPOP) for Higher Order Structure Characterization. |
| Q64098229 | Middle-way flexible docking: Pose prediction using mixed-resolution Monte Carlo in estrogen receptor α |
| Q48266709 | Orthogonal Mass Spectrometry-Based Footprinting for Epitope Mapping and Structural Characterization: The IL-6 Receptor upon Binding of Protein Therapeutics |
| Q42057094 | Predicting allosteric mutants that increase activity of a major antibiotic resistance enzyme |
| Q91646754 | Predicting allostery and microbial drug resistance with molecular simulations |
| Q89594473 | Predicting nitroimidazole antibiotic resistance mutations in Mycobacterium tuberculosis with protein engineering |
| Q47119795 | Prediction of New Stabilizing Mutations Based on Mechanistic Insights from Markov State Models |
| Q48139611 | Quantifying Allosteric Communication via Both Concerted Structural Changes and Conformational Disorder with CARDS. |
| Q107112104 | SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome |
| Q92890846 | Sodium-induced population shift drives activation of thrombin |
| Q52661545 | Structural and Mechanistic Basis for Extended-Spectrum Drug-Resistance Mutations in Altering the Specificity of TEM, CTX-M, and KPC β-lactamases. |
| Q57056883 | Synergistic effects of functionally distinct substitutions in β-lactamase variants shed light on the evolution of bacterial drug resistance |
| Q91964747 | The Role of the Ω-Loop in Regulation of the Catalytic Activity of TEM-Type β-Lactamases |
| Q53697056 | The antibiotic cyclomarin blocks arginine-phosphate-induced millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis. |
| Q64975394 | The dynamic conformational landscape of the protein methyltransferase SETD8. |
Search more.