Published in Sci Rep on August 19, 2016
UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem (2004) 112.47
Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J Mol Biol (1999) 15.00
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics (2013) 11.01
Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain. Science (1996) 9.48
Mechanism of coupled folding and binding of an intrinsically disordered protein. Nature (2007) 6.26
COMPUTING: Screen Savers of the World Unite! Science (2000) 3.54
DOCK 6: combining techniques to model RNA-small molecule complexes. RNA (2009) 2.75
Intrinsically disordered proteins in cellular signalling and regulation. Nat Rev Mol Cell Biol (2015) 2.69
Development and validation of a modular, extensible docking program: DOCK 5. J Comput Aided Mol Des (2006) 2.50
SHIFTX2: significantly improved protein chemical shift prediction. J Biomol NMR (2011) 2.47
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
Helical beta-peptide inhibitors of the p53-hDM2 interaction. J Am Chem Soc (2004) 2.15
Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase. J Med Chem (2008) 2.14
Structure-based design of novel inhibitors of the MDM2-p53 interaction. J Med Chem (2012) 2.01
Contemporary strategies for the stabilization of peptides in the alpha-helical conformation. Curr Opin Chem Biol (2008) 1.99
Structural basis for high-affinity peptide inhibition of p53 interactions with MDM2 and MDMX. Proc Natl Acad Sci U S A (2009) 1.94
Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery. Nat Chem (2014) 1.67
Transient protein states in designing inhibitors of the MDM2-p53 interaction. Structure (2013) 1.63
Disorder and residual helicity alter p53-Mdm2 binding affinity and signaling in cells. Nat Chem Biol (2014) 1.62
NMR-based protein potentials. Angew Chem Int Ed Engl (2010) 1.36
Identification of slow molecular order parameters for Markov model construction. J Chem Phys (2013) 1.34
Structure of free MDM2 N-terminal domain reveals conformational adjustments that accompany p53-binding. J Mol Biol (2005) 1.31
Structure of the stapled p53 peptide bound to Mdm2. J Am Chem Soc (2011) 1.30
Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9. J Chem Theory Comput (2013) 1.30
Markov state models of biomolecular conformational dynamics. Curr Opin Struct Biol (2014) 1.28
Quantitative lid dynamics of MDM2 reveals differential ligand binding modes of the p53-binding cleft. J Am Chem Soc (2008) 1.24
Evaluation of DOCK 6 as a pose generation and database enrichment tool. J Comput Aided Mol Des (2012) 1.22
Small-molecule inhibitors of the MDM2-p53 protein-protein interaction (MDM2 Inhibitors) in clinical trials for cancer treatment. J Med Chem (2014) 1.21
Systematic mutational analysis of peptide inhibition of the p53-MDM2/MDMX interactions. J Mol Biol (2010) 1.16
Perspective: Alchemical free energy calculations for drug discovery. J Chem Phys (2012) 1.10
Emerging methods for ensemble-based virtual screening. Curr Top Med Chem (2010) 1.08
DOCK 6: Impact of new features and current docking performance. J Comput Chem (2015) 1.07
Variational Approach to Molecular Kinetics. J Chem Theory Comput (2014) 1.05
Investigating how peptide length and a pathogenic mutation modify the structural ensemble of amyloid beta monomer. Biophys J (2012) 1.02
Dynamics of an intrinsically disordered protein reveal metastable conformations that potentially seed aggregation. J Am Chem Soc (2013) 0.96
A left-handed solution to peptide inhibition of the p53-MDM2 interaction. Angew Chem Int Ed Engl (2010) 0.96
In Silico Improvement of beta3-peptide inhibitors of p53 x hDM2 and p53 x hDMX. J Am Chem Soc (2009) 0.96
Markov state models provide insights into dynamic modulation of protein function. Acc Chem Res (2015) 0.94
Exploring the role of receptor flexibility in structure-based drug discovery. Biophys Chem (2013) 0.93
Discovery of multiple hidden allosteric sites by combining Markov state models and experiments. Proc Natl Acad Sci U S A (2015) 0.92
Emerging Computational Methods for the Rational Discovery of Allosteric Drugs. Chem Rev (2016) 0.92
An ultrahigh affinity d-peptide antagonist Of MDM2. J Med Chem (2012) 0.90
Variational cross-validation of slow dynamical modes in molecular kinetics. J Chem Phys (2015) 0.90
Improved coarse-graining of Markov state models via explicit consideration of statistical uncertainty. J Chem Phys (2012) 0.88
Rational design of topographical helix mimics as potent inhibitors of protein-protein interactions. J Am Chem Soc (2014) 0.87
On the Application of Molecular-Dynamics Based Markov State Models to Functional Proteins. J Chem Theory Comput (2014) 0.86
Autoinhibition of MDMX by intramolecular p53 mimicry. Proc Natl Acad Sci U S A (2015) 0.84
Modeling of arylamide helix mimetics in the p53 peptide binding site of hDM2 suggests parallel and anti-parallel conformations are both stable. PLoS One (2012) 0.83
Kinetic Distance and Kinetic Maps from Molecular Dynamics Simulation. J Chem Theory Comput (2015) 0.81
Microsecond simulations of mdm2 and its complex with p53 yield insight into force field accuracy and conformational dynamics. Proteins (2015) 0.80
Using Kinetic Network Models To Probe Non-Native Salt-Bridge Effects on α-Helix Folding. J Phys Chem B (2016) 0.79
Recognition Dynamics of p53 and MDM2: Implications for Peptide Design. J Phys Chem B (2016) 0.78
Probing the origin of structural stability of single and double stapled p53 peptide analogs bound to MDM2. Chem Biol Drug Des (2014) 0.78
How To Design a Successful p53-MDM2/X Interaction Inhibitor: A Thorough Overview Based on Crystal Structures. ChemMedChem (2015) 0.78
A spiroligomer α-helix mimic that binds HDM2, penetrates human cells and stabilizes HDM2 in cell culture. PLoS One (2012) 0.78
Configurational preferences of arylamide α-helix mimetics via alchemical free energy calculations of relative binding affinities. J Phys Chem B (2012) 0.78
Elucidation of Ligand-Dependent Modulation of Disorder-Order Transitions in the Oncoprotein MDM2. PLoS Comput Biol (2015) 0.77
Kinetic Network Models of Tryptophan Mutations in β-Hairpins Reveal the Importance of Non-Native Interactions. J Chem Theory Comput (2015) 0.77
Investigating Molecular Kinetics by Variationally Optimized Diffusion Maps. J Chem Theory Comput (2015) 0.77
Ensemble-Based Virtual Screening Led to the Discovery of New Classes of Potent Tyrosinase Inhibitors. J Chem Inf Model (2016) 0.77
Impact of Ser17 Phosphorylation on the Conformational Dynamics of the Oncoprotein MDM2. Biochemistry (2016) 0.76