Paolo Carloni
#163,375
Most Influential Person Now
Researcher
Paolo Carloni's AcademicInfluence.com Rankings
Paolo Carlonichemistry Degrees
Chemistry
#4777
World Rank
#5868
Historical Rank
Computational Chemistry
#51
World Rank
#51
Historical Rank
Chemical Engineering
#636
World Rank
#656
Historical Rank

Download Badge
Chemistry
Why Is Paolo Carloni Influential?
(Suggest an Edit or Addition)Paolo Carloni's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- Promoting transparency and reproducibility in enhanced molecular simulations (2019) (437)
- The role and perspective of ab initio molecular dynamics in the study of biological systems. (2002) (224)
- Coarse-grained model of proteins incorporating atomistic detail of the active site. (2005) (157)
- Potassium and sodium binding to the outer mouth of the K+ channel. (1999) (152)
- Accurate and efficient description of protein vibrational dynamics: Comparing molecular dynamics and Gaussian models (2004) (151)
- Unbinding Kinetics of a p38 MAP Kinase Type II Inhibitor from Metadynamics Simulations. (2017) (145)
- Substrate binding mechanism of HIV-1 protease from explicit-solvent atomistic simulations. (2009) (133)
- Drug resistance in HIV‐1 protease: Flexibility‐assisted mechanism of compensatory mutations (2002) (126)
- Electronic structure of wet DNA. (2002) (126)
- Key Steps of the cis-Platin-DNA Interaction: Density Functional Theory-Based Molecular Dynamics Simulations (2000) (125)
- Role of protein frame and solvent for the redox properties of azurin from Pseudomonas aeruginosa (2006) (124)
- Role of conformational fluctuations in the enzymatic reaction of HIV-1 protease. (2002) (121)
- Insights into the Binding of Phenyltiocarbamide (PTC) Agonist to Its Target Human TAS2R38 Bitter Receptor (2010) (120)
- Targeting biomolecular flexibility with metadynamics. (2010) (117)
- Water and potassium dynamics inside the KcsA K+ channel (2000) (117)
- Inhibition of α-Synuclein Fibrillization by Dopamine Is Mediated by Interactions with Five C-Terminal Residues and with E83 in the NAC Region (2008) (112)
- Bioinorganic chemistry of Parkinson's disease: structural determinants for the copper-mediated amyloid formation of alpha-synuclein. (2010) (109)
- Ab initio molecular dynamics-based assignment of the protonation state of pepstatin A/HIV-1 protease cleavage site. (2001) (106)
- Water at hydrophobic interfaces delays proton surface-to-bulk transfer and provides a pathway for lateral proton diffusion (2012) (95)
- Adaptive protein evolution grants organismal fitness by improving catalysis and flexibility (2008) (95)
- Cisplatin binding to DNA oligomers from hybrid Car-Parrinello/molecular dynamics simulations (2004) (94)
- Reaction Mechanism of HIV-1 Protease by Hybrid Car-Parrinello/Classical MD Simulations (2004) (89)
- A covalent PIN1 inhibitor selectively targets cancer cells by a dual mechanism of action (2017) (88)
- Conformational flexibility of the catalytic Asp dyad in HIV‐1 protease: An ab initio study on the free enzyme (2000) (85)
- Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations. (2007) (84)
- Target-related applications of first principles quantum chemical methods in drug design. (2006) (79)
- Calculation of redox properties: understanding short- and long-range effects in rubredoxin. (2007) (79)
- GOMoDo: A GPCRs Online Modeling and Docking Webserver (2013) (75)
- Polarization effects and charge transfer in the KcsA potassium channel. (2006) (75)
- Potassium permeation through the KcsA channel: a density functional study. (2002) (73)
- Role of zinc content on the catalytic efficiency of B1 metallo beta-lactamases. (2007) (73)
- Hypomorphic mutations in POLR3A are a frequent cause of sporadic and recessive spastic ataxia (2017) (72)
- Water-Assisted Reaction Mechanism of Monozinc β-Lactamases (2004) (72)
- Copper-1,10-phenanthroline complexes binding to DNA: structural predictions from molecular simulations. (2009) (71)
- Environmental and genetic factors support the dissociation between α-synuclein aggregation and toxicity (2016) (70)
- Solute-solvent charge transfer in aqueous solution. (2005) (70)
- STRUCTURE AND BONDING IN CISPLATIN AND OTHER PT(II) COMPLEXES (1995) (70)
- STRUCTURE AND BONDING IN CISPLATIN AND OTHER PT(II) COMPLEXES (1995) (70)
- Evolutionarily conserved functional mechanics across pepsin-like and retroviral aspartic proteases. (2005) (68)
- Coarse-Grained/Molecular Mechanics of the TAS2R38 Bitter Taste Receptor: Experimentally-Validated Detailed Structural Prediction of Agonist Binding (2013) (67)
- A comparative study of galactose oxidase and active site analogs based on QM/MM Car-Parrinello simulations (2000) (66)
- The Metallo-β-lactamase GOB Is a Mono-Zn(II) Enzyme with a Novel Active Site* (2007) (65)
- Coordination numbers of K(+) and Na(+) Ions inside the selectivity filter of the KcsA potassium channel: insights from first principles molecular dynamics. (2010) (64)
- Common structural traits across pathogenic mutants of the human prion protein and their implications for familial prion diseases. (2011) (63)
- On the Zwitterionic Nature of Gas-Phase Peptides and Protein Ions (2010) (62)
- Structure and function of vanadium haloperoxidases. (2006) (61)
- Conformational effects in protein electrospray-ionization mass spectrometry. (2016) (60)
- Modulation of Alpha-Synuclein Aggregation by Dopamine Analogs (2010) (59)
- Evidence for a Transient Additional Ligand Binding Site in the TAS2R46 Bitter Taste Receptor. (2015) (59)
- Convergent dynamics in the protease enzymatic superfamily. (2006) (58)
- The hydrolysis mechanism of the anticancer ruthenium drugs NAMI-A and ICR investigated by DFT-PCM calculations. (2008) (58)
- Dissociation of minor groove binders from DNA: insights from metadynamics simulations (2008) (57)
- Molecular Dynamics in Physiological Solutions: Force Fields, Alkali Metal Ions, and Ionic Strength. (2010) (57)
- Binding of novel azole-bridged dinuclear platinum(II) anticancer drugs to DNA: insights from hybrid QM/MM molecular dynamics simulations. (2006) (57)
- Copper binding to the N-terminally acetylated, naturally occurring form of alpha-synuclein induces local helical folding. (2015) (54)
- A Self-Activated Mechanism for Nucleic Acid Polymerization Catalyzed by DNA/RNA Polymerases. (2016) (52)
- A novel approach to the investigation of passive molecular permeation through lipid bilayers from atomistic simulations. (2012) (51)
- Enzymatic GTP hydrolysis: insights from an ab initio molecular dynamics study. (2002) (50)
- A structural model of agonist binding to the α3β4 neuronal nicotinic receptor (2003) (50)
- Common mechanistic features among metallo-beta-lactamases: a computational study of Aeromonas hydrophila CphA enzyme. (2009) (49)
- Exhaustive Search of Ligand Binding Pathways via Volume-Based Metadynamics. (2019) (49)
- RNA/Peptide Binding Driven by Electrostatics-Insight from Bidirectional Pulling Simulations. (2013) (49)
- Mesencephalic dopaminergic neurons express a repertoire of olfactory receptors and respond to odorant-like molecules (2014) (48)
- Structural facets of disease‐linked human prion protein mutants: A molecular dynamic study (2010) (48)
- The iron-sulfur cluster in the oxidized high-potential iron protein from Ectothiorhodospira halophila (1993) (47)
- Mechanism of Action of Cyclophilin A Explored by Metadynamics Simulations (2009) (47)
- Advanced Computational Methods in Molecular Medicine (2012) (46)
- Hybrid Molecular Mechanics/Coarse-Grained Simulations for Structural Prediction of G-Protein Coupled Receptor/Ligand Complexes (2012) (45)
- Molecular dynamics study of the KcsA channel at 2.0-A resolution: stability and concerted motions within the pore. (2004) (45)
- The unique fold and lability of the [2Fe-2S] clusters of NEET proteins mediate their key functions in health and disease (2018) (45)
- Computational study of the phosphoryl transfer catalyzed by a cyclin-dependent kinase. (2007) (45)
- Molecular Basis for Structural Heterogeneity of an Intrinsically Disordered Protein Bound to a Partner by Combined ESI-IM-MS and Modeling (2015) (44)
- Peptide aptamers targeting mutant p53 induce apoptosis in tumor cells. (2008) (43)
- A Computational Model for Protein Ionization by Electrospray Based on Gas-Phase Basicity (2012) (43)
- ELECTRONIC STRUCTURE OF THE CU, ZN SUPEROXIDE DISMUTASE ACTIVE SITE AND ITS INTERACTIONS WITH THE SUBSTRATE (1995) (41)
- Discovery of a Class of Diketopiperazines as Antiprion Compounds (2010) (40)
- Dynamics and energetics of water permeation through the aquaporin channel (2004) (40)
- Structural Determinants of the Prion Protein N-Terminus and Its Adducts with Copper Ions (2018) (40)
- Nicotine Blocks the Hyperpolarization-Activated Current Ih and Severely Impairs the Oscillatory Behavior of Oriens-Lacunosum Moleculare Interneurons (2010) (40)
- Reaction mechanism of caspases: Insights from QM/MM Car–Parrinello simulations (2003) (40)
- The C-terminal Src Inhibitory Kinase (Csk)-mediated Tyrosine Phosphorylation Is a Novel Molecular Mechanism to Limit P2X3 Receptor Function in Mouse Sensory Neurons* (2009) (39)
- Origin of proton affinity to membrane/water interfaces (2017) (39)
- Chasing the full free energy landscape of neuroreceptor/ligand unbinding by metadynamics simulations (2019) (39)
- Microseconds dynamics simulations of the outer-membrane protease T. (2008) (39)
- A hybrid TDDFT/MM investigation of the optical properties of aminocoumarins in water and acetonitrile solution (2003) (39)
- A homology model of the pore region of HCN channels. (2005) (39)
- Molecular motions in drug design: the coming age of the metadynamics method (2011) (37)
- Using metadynamics to understand the mechanism of calmodulin/target recognition at atomic detail. (2006) (37)
- Density functional theory studies on copper phenanthroline complexes. (2007) (36)
- Formamide Hydrolysis Investigated by Multiple-Steering ab Initio Molecular Dynamics (2004) (36)
- Nitrogen Fixation by a Molybdenum Catalyst Mimicking the Function of the Nitrogenase Enzyme: A Critical Evaluation of DFT and Solvent Effects. (2007) (36)
- Applications of density functional theory-based methods in medicinal chemistry (2002) (35)
- SELF-ASSEMBLED PEPTIDE NANOTUBES FROM FIRST PRINCIPLES (1997) (35)
- Local Fluctuations and Conformational Transitions in Proteins. (2012) (35)
- Molecular dynamics studies on superoxide dismutase and its mutants: the structural and functional role of Arg 143 (1992) (34)
- Substrate binding to mononuclear metallo‐β‐lactamase from Bacillus cereus (2004) (34)
- Crystal structure of the complex between carboxypeptidase A and the biproduct analog inhibitor L-benzylsuccinate at 2.0 A resolution. (1992) (34)
- Parallel synthesis, evaluation, and preliminary structure-activity relationship of 2,5-diamino-1,4-benzoquinones as a novel class of bivalent anti-prion compound. (2010) (34)
- Molecular dynamics studies on HIV‐1 protease: Drug resistance and folding pathways (2001) (34)
- Molecular dynamics studies on peroxidases: a structural model for horseradish peroxidase and a substrate adduct. (1994) (33)
- Docking Ligands on Protein Surfaces: The Case Study of Prion Protein. (2009) (33)
- Molecular modeling of ion channels: structural predictions. (2003) (33)
- Proton Dynamics in Protein Mass Spectrometry. (2017) (33)
- A molecular dynamics simulation-based interpretation of nuclear magnetic resonance multidimensional heteronuclear spectra of α-synuclein·dopamine adducts. (2013) (32)
- Nonempirical Calculations of a Hydrated RNA Duplex (1996) (32)
- Structural determinants and hydrogen-bond network of the mononuclear zinc(II)-β-lactamase active site (2002) (32)
- On the Oligomeric State of DJ-1 Protein and Its Mutants Associated with Parkinson Disease (2007) (32)
- Parameterization of azole‐bridged dinuclear platinum anticancer drugs via a QM/MM force matching procedure (2008) (31)
- Structure and dynamics of oligonucleotides in the gas phase. (2014) (31)
- Structural basis of gating of CNG channels (2005) (31)
- X-ray, NMR and molecular dynamics studies on reduced bovine superoxide dismutase: implications for the mechanism. (1994) (30)
- Ligand specificity of odorant receptors (2007) (30)
- Developing predictive rules for coordination geometry from visible circular dichroism of copper(II) and nickel(II) ions in histidine and amide main‐chain complexes (2014) (30)
- Conformational fluctuations of UreG, an intrinsically disordered enzyme. (2013) (30)
- Conformational ensemble of human α-synuclein physiological form predicted by molecular simulations. (2016) (29)
- Quantum medicinal chemistry (2003) (29)
- Extreme Scalability of DFT-based QM/MM MD Simulations Using MiMiC. (2019) (29)
- A Blueprint for High Affinity SARS-CoV-2 Mpro Inhibitors from Activity-Based Compound Library Screening Guided by Analysis of Protein Dynamics (2020) (29)
- Molecular dynamics simulations identify time scale of conformational changes responsible for conformational selection in molecular recognition of HIV-1 transactivation responsive RNA. (2014) (29)
- Dimethyl Phosphate: Stereoelectronic versus Environmental Effects (1999) (29)
- Protonation state and substrate binding to B2 metallo‐β‐lactamase CphA from Aeromonas hydrofila (2007) (29)
- Unwinding the helical linker of calcium‐loaded calmodulin: A molecular dynamics study (2005) (29)
- Density functional studies on herpes simplex virus type 1 thymidine kinase–substrate interactions: The role of Tyr‐172 and Met‐128 in thymine fixation (1998) (28)
- Molecular dynamics simulations on HiPIP from Chromatium vinosum and comparison with NMR data (1992) (28)
- Design of human granzyme B variants resistant to serpin B9 (2012) (28)
- Topologically Based Multipolar Reconstruction of Electrostatic Interactions in Multiscale Simulations of Proteins. (2008) (27)
- Dual binding mode of “bitter sugars” to their human bitter taste receptor target (2019) (27)
- On the Accuracy of Molecular Simulation-based Predictions of koff Values: A Metadynamics Study. (2020) (27)
- Computational Study of the DNA-Binding Protein Helicobacter pylori NikR: The Role of Ni2+2 2 Francesco Musiani and Branimir Bertoša contributed equally to the simulations presented here. (2010) (27)
- Molecular dynamics studies of caspase-3. (2003) (27)
- Azole-bridged diplatinum anticancer compounds. Modulating DNA flexibility to escape repair mechanism and avoid cross resistance. (2007) (27)
- The Role and Perspective of ab initio Molecular Dynamics in the Study of Biological Systems (2002) (27)
- Predicting ligand binding poses for low-resolution membrane protein models: Perspectives from multiscale simulations. (2018) (26)
- Understanding Ligand Binding to G-Protein Coupled Receptors Using Multiscale Simulations (2019) (26)
- The Rational of Catalytic Activity of Herpes Simplex Virus Thymidine Kinase (2001) (25)
- Salt effects on water/hydrophobic liquid interfaces: a molecular dynamics study (2012) (25)
- Permeation through the Cell Membrane of a Boron-Based β-Lactamase Inhibitor (2011) (25)
- Agonist Binding to Chemosensory Receptors: A Systematic Bioinformatics Analysis (2017) (25)
- Platination of the copper transporter ATP7A involved in anticancer drug resistance. (2014) (25)
- Molecular dynamics simulations of the NGF-TrkA domain 5 complex and comparison with biological data. (2003) (25)
- Conformations of the Huntingtin N‐term in aqueous solution from atomistic simulations (2011) (25)
- MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry. (2019) (24)
- A small chemical library of 2-aminoimidazole derivatives as BACE-1 inhibitors: Structure-based design, synthesis, and biological evaluation. (2012) (24)
- Arginine–phosphate salt bridges in protein–DNA complexes: a Car–Parrinello study (2001) (24)
- Regulation of Bestrophins by Ca2+: A Theoretical and Experimental Study (2009) (24)
- Structural role of compensatory amino acid replacements in the α-synuclein protein. (2011) (24)
- Duocarmycins binding to DNA investigated by molecular simulation. (2006) (24)
- A proficient enzyme: insights on the mechanism of orotidine monophosphate decarboxylase from computer simulations. (2004) (23)
- Counterion Redistribution upon Binding of a Tat-Protein Mimic to HIV-1 TAR RNA. (2012) (23)
- Second step of hydrolytic dehalogenation in haloalkane dehalogenase investigated by QM/MM methods (2008) (23)
- Serine proteases: An ab initio molecular dynamics study (1999) (23)
- Anthramycin-DNA binding explored by molecular simulations. (2006) (23)
- The balancing act of NEET proteins: Iron, ROS, calcium and metabolism. (2020) (23)
- The metallo-beta-lactamase GOB is a mono-Zn(II) enzyme with a novel active site. (2007) (23)
- Understanding and Controlling Food Protein Structure and Function in Foods: Perspectives from Experiments and Computer Simulations. (2020) (23)
- α-Synuclein phosphorylation at serine 129 occurs after initial protein deposition and inhibits seeded fibril formation and toxicity (2022) (22)
- Sliding of alkylating anticancer drugs along the minor groove of DNA: new insights on sequence selectivity. (2008) (22)
- G protein inactive and active forms investigated by simulation methods (2009) (22)
- Molecular dynamics studies on mutants of Cu, Zn superoxide dismutase: The functional role of charged residues in the electrostatic loop VII (1994) (22)
- Structural Determinants of Cisplatin and Transplatin Binding to the Met-Rich Motif of Ctr1: A Computational Spectroscopy Approach. (2012) (22)
- Origin of functional diversity among tetrameric voltage‐gated channels (2006) (21)
- Molecular recognition of DNA by ligands: roughness and complexity of the free energy profile. (2013) (21)
- Carboplatin versus cisplatin: density functional approach to their molecular properties (1995) (21)
- Structural Determinants for the Binding of Morphinan Agonists to the μ-Opioid Receptor (2015) (21)
- Protonation state of Asp120 in the binuclear active site of the metallo-beta-lactamase from Bacteroides fragilis. (2003) (21)
- Cation-π versus OH-π Interactions in Proteins: A Density Functional Study (2000) (20)
- Ab initio molecular dynamics studies on HIV‐1 reverse transcriptase triphosphate binding site: Implications for nucleoside‐analog drug resistance (2000) (20)
- A Strategically Located Arg/Lys Residue Promotes Correct Base Paring During Nucleic Acid Biosynthesis in Polymerases. (2018) (20)
- Reducing Mutant Huntingtin Protein Expression in Living Cells by a Newly Identified RNA CAG Binder. (2018) (20)
- Ab initio molecular dynamics studies of a synthetic biomimetic model of galactose oxidase (1999) (20)
- Copper(II) and the pathological H50Q α-synuclein mutant: Environment meets genetics (2017) (20)
- Role of phosphorylated Thr160 for the activation of the CDK2/Cyclin A complex (2005) (19)
- Molecular simulation of the binding of nerve growth factor peptide mimics to the receptor tyrosine kinase A. (2006) (19)
- Simulations of enzymatic systems: Perspectives from Car-Parrinello molecular dynamics simulations (2001) (19)
- Statistical analysis of σ-holes: a novel complementary view on halogen bonding. (2014) (19)
- TETRAETHYLAMMONIUM BINDING TO THE OUTER MOUTH OF THE KcsA POTASSIUM CHANNEL: IMPLICATIONS FOR ION PERMEATION (2002) (19)
- Structural properties of polyglutamine aggregates investigated via molecular dynamics simulations. (2008) (19)
- Rare FLT3 deletion mutants may provide additional treatment options to patients with AML: an approach to individualized medicine (2015) (19)
- Carnosine and Homocarnosine Degradation Mechanisms by the Human Carnosinase Enzyme CN1: Insights from Multiscale Simulations. (2016) (18)
- Binding of phosphinate and phosphonate inhibitors to aspartic proteases: a first-principles study. (2006) (18)
- Drug-Target Binding Investigated by Quantum Mechanical/Molecular Mechanical (QM/MM) Methods (2006) (18)
- Synthesis and evaluation of a library of 2,5-bisdiamino-benzoquinone derivatives as probes to modulate protein-protein interactions in prions. (2010) (18)
- Amino acid modification in the HIV-1 Tat basic domain: insights from molecular dynamics and in vivo functional studies. (2002) (18)
- Open Boundary Simulations of Proteins and Their Hydration Shells by Hamiltonian Adaptive Resolution Scheme. (2017) (18)
- Role of Prion Disease-Linked Mutations in the Intrinsically Disordered N-Terminal Domain of the Prion Protein. (2013) (18)
- cAMP Modulation of the cytoplasmic domain in the HCN2 channel investigated by molecular simulations. (2006) (18)
- Molecular dynamics calculations on peroxidases: the effect of calcium ions on protein structure (1996) (18)
- Molecular Dynamics Simulations of the [2Fe–2S] Cluster-Binding Domain of NEET Proteins Reveal Key Molecular Determinants That Induce Their Cluster Transfer/Release (2017) (17)
- Hydrogen Bonding Cooperativity in polyQ β-Sheets from First Principle Calculations. (2010) (17)
- Structural heterogeneity of the μ-opioid receptor’s conformational ensemble in the apo state (2017) (17)
- Permeability Coefficients of Lipophilic Compounds Estimated by Computer Simulations. (2016) (17)
- A novel class of peptides with facilitating action on neuronal nicotinic receptors of rat chromaffin cells in vitro: functional and molecular dynamics studies. (2002) (16)
- Molecular view of ligands specificity for CAG repeats in anti-Huntington therapy. (2015) (16)
- On the nature of the reaction intermediate in the HIV-1 protease: a quantum chemical study (2008) (16)
- Comparative analysis of HIV‐1 Tat variants (2004) (16)
- Protein design is a key factor for subunit-subunit association. (1999) (15)
- Conformational analysis of dimethyl phosphate in aqueous solution: a density functional theory-based molecular dynamics study (1999) (15)
- Molecular dynamics simulations on HIV-1 Tat (2004) (15)
- Computational metallomics of the anticancer drug cisplatin. (2015) (15)
- Catabolite activator protein in aqueous solution: a molecular simulation study. (2007) (15)
- Role of the Membrane Dipole Potential for Proton Transport in Gramicidin A Embedded in a DMPC Bilayer. (2013) (15)
- Ser133 phosphate-KIX interactions in the CREB-CBP complex: an ab initio molecular dynamics study (2000) (14)
- Regulation of adenylyl cyclase 5 in striatal neurons confers the ability to detect coincident neuromodulatory signals (2019) (14)
- Calcium binding to the transmembrane domain of the sarcoplasmic reticulum Ca2+‐ATPase: Insights from molecular modeling (2002) (14)
- Molecular dynamics simulations of outer-membrane protease T from E. coli based on a hybrid coarse-grained/atomistic potential (2006) (14)
- Insights on HIV‐1 Tat:P/CAF bromodomain molecular recognition from in vivo experiments and molecular dynamics simulations (2005) (14)
- Large-scale motions and electrostatic properties of furin and HIV-1 protease. (2007) (14)
- Target-Related Applications of First Principles Quantum Chemical Methods in Drug Design (2006) (14)
- NMR Studies of Hetero-Association of Caffeine with di-O-Caffeoylquinic Acid Isomers in Aqueous Solution (2014) (14)
- Structural biology of cisplatin complexes with cellular targets: the adduct with human copper chaperone atox1 in aqueous solution. (2014) (14)
- Novel angiogenin mutants with increased cytotoxicity enhance the depletion of pro-inflammatory macrophages and leukemia cells ex vivo (2015) (13)
- Anthrax Lethal Factor Investigated by Molecular Simulations. (2008) (13)
- Structural Prediction of the Dimeric Form of the Mammalian Translocator Membrane Protein TSPO: A Key Target for Brain Diagnostics (2018) (13)
- Sequential Virtual Screening Approach to the Identification of Small Organic Molecules as Potential BACE‐1 Inhibitors (2011) (13)
- Enhanced-Sampling Simulations for the Estimation of Ligand Binding Kinetics: Current Status and Perspective (2022) (13)
- Molecular Simulation-Based Structural Prediction of Protein Complexes in Mass Spectrometry: The Human Insulin Dimer (2014) (13)
- DFT modeling of biological systems (2006) (13)
- Multiple Steering Molecular Dynamics Applied to Water Exchange at Alkali Ions (2002) (13)
- Computational molecular biology approaches to ligand‐target interactions (2009) (12)
- Open-Boundary Molecular Mechanics/Coarse-Grained Framework for Simulations of Low-Resolution G-Protein-Coupled Receptor–Ligand Complexes (2019) (12)
- Structure/function relationships of phospholipases C Beta. (2013) (12)
- Ligand binding to anti-cancer target CD44 investigated by molecular simulations (2016) (12)
- Targeted Free Energy Perturbation Revisited: Accurate Free Energies from Mapped Reference Potentials. (2021) (12)
- Computational Study of the DNA-Binding Protein Helicobacter pylori NikR: The Role of Ni(2.). (2010) (12)
- Hybrid Lipoic Acid Derivatives to Attack Prion Disease on Multiple Fronts (2011) (12)
- Molecular basis of CLC antiporter inhibition by fluoride. (2020) (12)
- Unifying view of mechanical and functional hotspots across class A GPCRs (2017) (12)
- High-throughput screening discovers antifibrotic properties of haloperidol by hindering myofibroblast activation. (2019) (12)
- Structural prediction of a rhodamine-based biosensor and comparison with biophysical data. (2013) (12)
- Many-Body Perturbation Theory Extended to the Quantum Mechanics/Molecular Mechanics Approach: Application to Indole in Water Solution. (2009) (11)
- Dominant-negative effects in prion diseases: insights from molecular dynamics simulations on mouse prion protein chimeras (2013) (11)
- Role of Extracellular Loops and Membrane Lipids for Ligand Recognition in the Neuronal Adenosine Receptor Type 2A: An Enhanced Sampling Simulation Study (2018) (11)
- Effect of in vivo post-translational modifications of the HMGB1 protein upon binding to platinated DNA: a molecular simulation study (2018) (11)
- Engineered human angiogenin mutations in the placental ribonuclease inhibitor complex for anticancer therapy: Insights from enhanced sampling simulations (2016) (10)
- Molecular basis of the allosteric mechanism of cAMP in the regulatory PKA subunit (2005) (10)
- Molecular Recognition of Platinated DNA from Chromosomal HMGB1. (2014) (10)
- Sequence-dependent structural properties of B-DNA: what have we learned in 40 years? (2021) (10)
- HIV-1 Integrase–DNA Interactions Investigated by Molecular Modelling (2008) (10)
- Insight into the Mechanism of Intramolecular Inhibition of the Catalytic Activity of Sirtuin 2 (SIRT2) (2015) (10)
- X-ray diffraction studies on carboxypeptidase A complexes: the zinc stereochemistry (1992) (10)
- A structural model of agonist binding to the alpha3beta4 neuronal nicotinic receptor. (2003) (9)
- HIV-1 Tat Binding to PCAF Bromodomain: Structural Determinants from Computational Methods (2012) (9)
- Molecular modeling studies on CNG channel from bovine retinal rod: A structural model of the cyclic nucleotide‐binding domain (2003) (9)
- Deuterium isotope effects in A:T and A:U base pairs: a computational NMR study. (2006) (9)
- Multi-scale simulations of membrane proteins: The case of bitter taste receptors (2017) (9)
- NADH interactions with WT‐ and S94A‐acyl carrier protein reductase from Mycobacterium tuberculosis: An ab initio study (2002) (9)
- Water-Triggered, Irreversible Conformational Change of SARS-CoV-2 Main Protease on Passing from the Solid State to Aqueous Solution (2021) (9)
- Enhanced Sampling Approach to the Induced-Fit Docking Problem in Protein-Ligand Binding: The Case of Mono-ADP-Ribosylation Hydrolase Inhibitors. (2021) (9)
- Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study (2018) (9)
- Proton dynamics in an enzyme model substrate: an ab initio molecular dynamics study (2000) (9)
- Vibrational Energy in Proteins Correlates with Topology. (2018) (9)
- Density Functional Theory‐Based Molecular Dynamics of Biological Systems (2002) (8)
- Engineered Versions of Granzyme B and Angiogenin Overcome Intrinsic Resistance to Apoptosis Mediated by Human Cytolytic Fusion Proteins (2015) (8)
- Common Mechanistic Features among Metallo-β-lactamases (2009) (8)
- Structure and Raman spectrum of clavulanic acid in aqueous solution. (2007) (8)
- Water-assisted reaction mechanism of monozinc beta-lactamases. (2004) (8)
- Interfacial water molecules at biological membranes: Structural features and role for lateral proton diffusion (2018) (8)
- Multiscale simulations on human Frizzled and Taste2 GPCRs. (2019) (8)
- Designing the Sniper: Improving Targeted Human Cytolytic Fusion Proteins for Anti-Cancer Therapy via Molecular Simulation (2017) (8)
- Spectroscopic Properties of Formaldehyde in Aqueous Solution: Insights from Car-Parrinello and TDDFT/CASPT2 Calculations. (2010) (8)
- Rational approach to an antiprion compound with a multiple mechanism of action. (2015) (8)
- On the accuracy of molecular simulation-based predictions of koff values: a Metadynamics study (2020) (7)
- DNA like-charge attraction and overcharging by divalent counterions in the presence of divalent co-ions (2016) (7)
- Spinocerebellar ataxia type 14: refining clinicogenetic diagnosis in a rare adult‐onset disorder (2021) (7)
- Structure-function relationships of the disease-linked A218T oxytocin receptor variant (2022) (7)
- Theoretical optical spectroscopy of complex systems (2013) (7)
- EXAFS study of the active site of alkaline phosphatase from E. coli (1992) (7)
- On the active site of mononuclear B1 metallo β-lactamases: a computational study (2012) (7)
- Computational studies on the prion protein. (2013) (6)
- Hybrid MM/CG Webserver: Automatic Set Up of Molecular Mechanics/Coarse-Grained Simulations for Human G Protein-Coupled Receptor/Ligand Complexes (2020) (6)
- Coevolutionary data-based interaction networks approach highlighting key residues across protein families: The case of the G-protein coupled receptors (2020) (6)
- In silico/in vitro screening and hit evaluation identified new phenothiazine anti-prion derivatives. (2020) (6)
- An anti-diabetic drug targets NEET (CISD) proteins through destabilization of their [2Fe-2S] clusters (2022) (6)
- Insights on the acetylated NF‐κB transcription factor complex with DNA from molecular dynamics simulations (2012) (6)
- Localizing the Charged Side Chains of Ion Channels within the Crowded Charge Models. (2013) (6)
- Robust principal component analysis‐based prediction of protein‐protein interaction hot spots (2021) (6)
- Quantum Medicinal Chemistry: CARLONI:QUANTUM MED.CHEM. (2003) (6)
- Structural Role of Compensatory Aminoacid Replacements in the Alpha- Synuclein Protein (2011) (6)
- Ligand Pose Predictions for Human G Protein-Coupled Receptors: Insights from the Amber-Based Hybrid Molecular Mechanics/Coarse-Grained Approach (2020) (5)
- Structural Modeling of Human Prion Protein's Point Mutations. (2017) (5)
- Molecular dissection of human oncostatin M-mediated signal transductions through site-directed mutagenesis. (2009) (5)
- Innovative Non-PrP-Targeted Drug Strategy Designed to Enhance Prion Clearance (2022) (5)
- Expanding the boundaries of ligand–target modeling by exascale calculations (2021) (5)
- 9.15 – Bioinformatics (2010) (5)
- Ion permeation in the NanC porin from Escherichia coli: free energy calculations along pathways identified by coarse-grain simulations. (2013) (5)
- Changes in non-core regions stabilise plastocyanin from the thermophilic cyanobacterium Phormidium laminosum (2010) (5)
- Structural predictions of neurobiologically relevant G-protein coupled receptors and intrinsically disordered proteins. (2015) (5)
- A gate mechanism indicated in the selectivity filter of the potassium channel KscA (2007) (5)
- EXAFS studies of Fe(III)-phosvitin at high metal to protein ratios (1994) (4)
- Mechanisms Underlying Proton Release in CLC-type F-/H+ Antiporters. (2021) (4)
- MiMiC: Multiscale Modeling in Computational Chemistry (2020) (4)
- X-ray diffraction study of the interaction between carboxypeptidase A and (S)-(+)-1-amino-2-phenylethyl phosphonic acid. (1992) (4)
- Substrate binding to mononuclear metallo-beta-lactamase from Bacillus cereus. (2004) (4)
- Molecular Dynamics-Assisted Interpretation of Experimentally Determined Intrinsically Disordered Protein Conformational Components: The Case of Human α-Synuclein. (2022) (4)
- Partially folded states of HIV-1 protease: Molecular dynamics simulations and ligand binding (2006) (4)
- Structural models of human big conductance calcium- and voltage-gated potassium channels (2007) (4)
- The Asn 38-Cys 84 H-bond in plastocyanin (2004) (4)
- Molecular Mechanics/Coarse-Grained Models (2014) (4)
- Structural prediction of the interaction of the tumor suppressor p27KIP1 with cyclin A/CDK2 identifies a novel catalytically relevant determinant (2017) (4)
- Impact of Cholesterol on the Stability of Monomeric and Dimeric Forms of the Translocator Protein TSPO: A Molecular Simulation Study (2020) (4)
- Chemosensorial G-proteins-coupled receptors: a perspective from computational methods. (2014) (4)
- The two redox states of the human NEET proteins’ [2Fe–2S] clusters (2021) (4)
- Aromaticity at position 39 in α‐synuclein: A modulator of amyloid fibril assembly and membrane‐bound conformations (2022) (4)
- Multi-scale modeling of HIV-1 proteins (2009) (3)
- The Interplay of Cholesterol and Ligand Binding in hTSPO from Classical Molecular Dynamics Simulations (2021) (3)
- Many‐body meets QM/MM: Application to indole in water solution (2008) (3)
- Role of Tyr-39 for the Structural Features of α-Synuclein and for the Interaction with a Strong Modulator of Its Amyloid Assembly (2020) (3)
- Chapter 9. First Principles Methods in Biology: From Continuum Models to Hybrid Ab initio Quantum Mechanics/Molecular Mechanics (2016) (3)
- - Molecular Mechanics/Coarse-Grained Simulations as a Structural Prediction Tool for GPCRs/Ligand Complexes (2015) (3)
- Binding of Zn(II) to Tropomyosin Receptor Kinase A in Complex with Its Cognate Nerve Growth Factor: Insights from Molecular Simulation and in Vitro Essays. (2018) (3)
- Molecular Mechanics / Coarse-grain simulations as a structural prediction tool for GPCRs / ligand complexes (2013) (3)
- QM/MM Car-Parrinello molecular dynamics study of selectivity in a potassium channel (2004) (3)
- Role of hydrophobic residues for the gaseous formation of helical motifs. (2019) (2)
- Density-Functional Theory Investigations of Enzyme-substrate Interactions (2002) (2)
- Mechanism of Calcium Permeation in a Glutamate Receptor Ion Channel (2023) (2)
- Role and Perspective of Molecular Simulation-Based Investigation of RNA–Ligand Interaction: From Small Molecules and Peptides to Photoswitchable RNA Binding (2021) (2)
- Cation Selectivity in Biological Cation Channels Using Experimental Structural Information and Statistical Mechanical Simulation (2015) (2)
- Biomolecular Simulation: A Perspective from High Performance Computing (2020) (2)
- Multiscale molecular simulations to investigate adenylyl cyclase‐based signaling in the brain (2022) (2)
- Corrigendum to “Common Structural Traits across Pathogenic Mutants of the Human Prion Protein and Their Implications for Familial Prion Diseases” [J. Mol. Biol. 411 (2011) 700–712] (2012) (2)
- Cover Picture: Discovery of a Class of Diketopiperazines as Antiprion Compounds (ChemMedChem 8/2010) (2010) (2)
- EXAFS investigation on nickel substituted Cu,Zn bovine superoxide dismutase (1994) (2)
- Dynamics and energetics of water permeation through the aquaporin channel (2)
- Multiple Poses and Thermodynamics of Ligands Targeting Protein Surfaces: The Case of Furosemide Binding to mitoNEET in Aqueous Solution (2022) (2)
- Electrostatic role of phosphate 2485 in the large ribosomal unit from H. marismortui (2003) (2)
- Hydration of chloride anions in the NanC Porin from Escherichia coli: a comparative study by QM/MM and MD simulations. (2014) (2)
- Trapping acrylamide by a Michael addition: A computational study of the reaction between acrylamide and niacin (2014) (2)
- Molecular Dynamics and Structural Studies of Zinc Chloroquine Complexes (2022) (1)
- Modeling the allosteric modulation on a G-Protein Coupled Receptor: the case of M2 muscarinic Acetylcholine Receptor in complex with LY211960 (2020) (1)
- Catalytic Mechanism of Metallo β‐Lactamases: Insights from Calculations and Experiments (2010) (1)
- Investigating targets for neuropharmacological intervention by molecular dynamics simulations. (2019) (1)
- HIV-1 integrase binding to its cellular partners: a perspective from computational biology. (2014) (1)
- On the Domain of Applicability of Currently used Force Fields for the Calculation of the Activity of Alkali Ions at Physiological Ionic Strength (2010) (1)
- Ligand Affinities within the Open-Boundary Molecular Mechanics/Coarse-Grained Framework (I): Alchemical Transformations within the Hamiltonian Adaptive Resolution Scheme. (2021) (1)
- Mesencephalic dopaminergic neurons express a repertoire of olfactory receptors and respond to odorant-like molecules (2014) (1)
- NEET proteins as novel drug targets for mitochondrial dysfunction (2021) (1)
- Molecular Simulation Studies of Proteins Involved in Parkinson's Disease (2008) (1)
- Hybrid Molecular Mechanics/Coarse-Grained Calculations Applied to GPCR Receptors (2012) (1)
- Corrigendum: Cover Picture: Discovery of a Class of Diketopiperazines as Antiprion Compounds (ChemMedChem 8/2010) (2010) (1)
- Acrylamide Binding to Its Cellular Targets: Insights from Computational Studies (2011) (1)
- Editor's Note: Peptide Aptamers Targeting Mutant p53 Induce Apoptosis in Tumor Cells. (2022) (1)
- Publisher's Note: “Molecular recognition of DNA by ligands: Roughness and complexity of the free energy profile” [J. Chem. Phys. 139, 145102 (2013)] (2013) (1)
- SCIENTIFIC HIGHLIGHT OF THE MONTH : ” Ab Initio Modeling of Biological Systems ” Ab Initio Modeling of Biological Systems (1)
- In silico study of putative calcium-binding domains in hBK and hBest1 (2007) (0)
- The Two Faces of Bitter Sugars: Insights from Multiscale Simulations (2019) (0)
- Molecular determinants of acrylamide neurotoxicity through covalent docking (2023) (0)
- Correction to: Fluoride Transport and Inhibition Across CLC Transporters. (2022) (0)
- Large Scale Car-Parrinello Simulation of Fully Hydrated DNA (2003) (0)
- Monovalent monatomic ions in biological environments : insights from computational biophysics studies (2013) (0)
- Copper complex-DNA lnteractions: molecular simulations studies. (2014) (0)
- Huntingtin: Stability and Interaction with Molecular Partner from Computational Biophysics Studies (2010) (0)
- Assessment of the Structure of Protein-Protein Complexes Using Computational Methods (2015) (0)
- Molecular Simulations of NGF Protein (2013) (0)
- Cover Image, Volume 13, Issue 1 (2023) (0)
- Role of membrane composition and the extracellular loops for ligand binding to the neuronal human adenosine receptor type 2A (2017) (0)
- StructuralModelsofHumanBigConductanceCalcium-and Voltage-gatedPotassiumChannels (2007) (0)
- Understanding anticancer Drug-DNA interactions via molecular dynamics simulations (2007) (0)
- Back Cover: Structural Biology of Cisplatin Complexes with Cellular Targets: The Adduct with Human Copper Chaperone Atox1 in Aqueous Solution (Chem. Eur. J. 37/2014) (2014) (0)
- Hybrid Car-Parrinello Molecular Dynamics/Molecular Mechanics Simulations: a Powerful Tool for the Investigation of Biological Systems (2012) (0)
- Computational study of the dimethylphosphate hydrolysis as thereference system for the understanding of the restrictionendonucleases mechanism (2011) (0)
- Predicting conformational ensembles of the intrinsically disordered protein α-Synuclein via molecular simulation (2014) (0)
- Metadynamics simulations of ligands binding to proteins’ surfaces: a novel tool for rational drug design (2023) (0)
- Ion Selectivity in Voltage-gated Biological Ion Channels (2014) (0)
- The Role of Native State Topology in Protein Folding and Dynamics (2001) (0)
- DNA like-charge attraction and overcharging by divalent counterions in the presence of divalent co-ions (2017) (0)
- Interactions of HIV-1 proteins with their cellular partners : insights from computational methods (2013) (0)
- Hybrid QM/MM molecular dynamics simulation in drug-DNA interactions (2004) (0)
- Fluoride Transport and Inhibition Across CLC Transporters. (2022) (0)
- Impact of Cholesterol on the Stability of Monomeric 2 and Dimeric Forms of the Translocator Protein TSPO: (2020) (0)
- Corrigendum to “X-ray, NMR and molecular dynamics studies on reduced bovine superoxide dismutase: Implications for the mechanism” [Biochem. Biophys. Res. Commun. 202 (1994) 1088–1095] (2012) (0)
- MiMiCPy: An Efficient Toolkit for MiMiC-Based QM/MM Simulations (2023) (0)
- Proton Transfers to DNA in Native Electrospray Ionization Mass Spectrometry: A QM/MM Study (2022) (0)
- Generation and characterization of angiogenin mutants as improved effector domains for H22(scFv)-based cytolytic fusion proteins (2017) (0)
- Origin of proton affinity to membrane/water interfaces (2017) (0)
- Investigating functional aspects and inhibition of the human carnosinase CN1 enzyme by computational methods (2017) (0)
- Modeling and Design of Molecular Materials 2014 (2014) (0)
- Multiscale simulation-based structural predictions of metalloproteins of pharmacological relevance (2017) (0)
- Molecular Mechanics/ Coarse{Grained hybrid model for investigating protein function (2007) (0)
- A novel parametrization scheme for classical and quantum mechanical simulations of large, floppy molecular systems (2006) (0)
- Action of the anticancer drug cisplatin investigated by molecular simulation (2013) (0)
- QM and QM/MM studies of the phosphoryl transfer reaction catalyzed by a cyclin-dependent kinase (CDKs) (2004) (0)
- Duocarmycins binding to DNA explored by molecular simulation (2005) (0)
- Computational studies on DNA recognition of novel organic and copper anti-tumor compounds (2013) (0)
- Modelling eNvironment for Isoforms (MoNvIso): A general platform to predict structural determinants of protein isoforms in genetic diseases (2022) (0)
- Exploring the transport cycle of DgoT, a bacterial homolog of human vesicular glutamate transporters. (2023) (0)
- Finding common structural traits of GPCRs by computational molecular biology approaches (2016) (0)
- Molecular Recognition Routes Of DNA By Anticancer Ligands: Mechanisms and Free Energies Explored Via Molecular Dynamics Simulations (2009) (0)
- Modeling the allosteric modulation on a G-Protein Coupled Receptor: the case of M2 muscarinic Acetylcholine Receptor in complex with LY211960 (2020) (0)
- Dual binding mode of “bitter sugars” to their human bitter taste receptor target (2019) (0)
- Predictions of the Poses and Affinity of a Ligand over the Entire Surface of a NEET Protein: The Case of Human MitoNEET (2023) (0)
- Modelling protein-protein interactions in neuronal signalling pathways via coarse-grained and atomistic docking approaches (2014) (0)
- 18F-labelled probes for non-invasive assessment of the IDH genotype in diffuse glioma (2022) (0)
- A model of N-terminal Cyclin T1 based on FRET experiments (2005) (0)
- Excited-state properties calculations: Applications to biological systems (2009) (0)
- Impact of Phosphorylation on alpha-Synuclein Structural Determinants (2023) (0)
- Supraligand fine tuning of Zn-based enzymes: the case of Horse Liver alcohol dehydrogenase (2001) (0)
- Microseconds protein-ligand molecular dynamics simulations by using a hybrid force field (2007) (0)
- Long-range compaction and organization of interphase chromatin in budding yeast (2005) (0)
- Author response for "Robust Principal Component Analysis‐based Prediction of Protein‐Protein Interaction Hot spots ( RBHS )" (2020) (0)
- Binding of F-19848A and Natural Compounds to CD44: Implications to Breast Cancer (2015) (0)
- Novel Deletion Mutants in the Juxtamembrane Domain of Fms-like Tyrosine Kinase 3 (FLT3) Induce Transformation By Release from Autoinhibition in AML (2014) (0)
- Conformational footprinting of proteins using a combination of top-down electron transfer dissociation and ion mobility (2018) (0)
- Abstract 5545: Molecular Dissection of Human Oncostatin M-Mediated Signal Transductions Through Site-Directed Mutagenesis (2008) (0)
- Simulations of Copper-1,10-Phenanthroline Complexes Binding the DNA (2009) (0)
- Structural aspects of the Huntingtin protein investigated by biocomputing methods (2011) (0)
- Molecular Simulation Approaches to Proteins Structure and Dynamics and to Ligand Design (2006) (0)
- Design and synthesis of a library of benzoquinone derivatives as probes to modulate protein-protein interactions in prions (2008) (0)
- Synthesis and Evaluation of a Library of 2,5-Bisdiamino-benzoquinone Derivatives as Probes to Modulate Protein—Protein Interactions in Prions. (2010) (0)
- A Simulative Model for the Analysis of Conduction Properties of Ion Channels Based on First-Principle Approaches (2004) (0)
- Scalability of 3D-DFT by block tensor-matrix multiplication on the JUWELS Cluster (2023) (0)
- Atomistic Simulation Studies of the Permeation of Organic Molecules Through Lipid Membranes (2012) (0)
- Outline of the book (2003) (0)
- Multimap targeted free energy estimation (2023) (0)
- Biocomputing approaches to protein protein interactions in molecular medicine (2013) (0)
- Structural prediction of the interaction of the tumor suppressor p27KIP1 with cyclin A/CDK2 identifies a novel catalytically relevant determinant (2017) (0)
- Ab Initio Molecular Dynamics Simulations of Biologically Relevant Systems (2005) (0)
- Computer–aided design of ligands targeting RNA polyCAG expansion tracts in Huntington’s disease (2014) (0)
- Proton Transfers to DNA in Native Electrospray Ionization Mass Spectrometry: A Quantum Mechanics/Molecular Mechanics Study (2022) (0)
- Machine Learning-aided Discovery of Novel Chemotype Antagonists for G Protein-coupled Receptors: The Case of the Adenosine A2A Receptor (2023) (0)
- From Computational Biophysics to Systems Biology (CBSB11) Celebrating Harold Scheragas 90th Birthday (2012) (0)
- X-ray studies of the binding of small anionic inhibitors at the carboxypeptidase A active site. (1991) (0)
- Receptors' Mosaics and Allostery for Pharmacology (2020) (0)
- Understanding and Controlling Food Protein Folding and Aggregation and taste: perspectives from experiment and simulation (0)
- The unique fold and lability of the [2Fe-2S] clusters of NEET proteins mediate their key functions in health and disease (2018) (0)
- Theoretical Studies on the KcsA Potassium Channel (2000) (0)
- Structure-Based Screening Reveals a Ligand That Stabilizes the [2Fe-2S] Clusters of Human mitoNEET and Reduces Ovarian Cancer Cell Proliferation. (2022) (0)
- Molecular simulations studies on human NEET proteins, novel targets for pharmaceutical intervention (2020) (0)
- An Enhanced Sampling Approach to the Induced Fit Docking Problem in Protein-Ligand Binding: the case of mono-ADP-ribosylation hydrolases inhibitors (2021) (0)
- Computational studies on seven helix transmembrane receptors (2013) (0)
This paper list is powered by the following services:
What Schools Are Affiliated With Paolo Carloni?
Paolo Carloni is affiliated with the following schools: