Paolo Carloni

Paolo Carloni's AcademicInfluence.com Rankings

Paolo Carloni

Chemistry

#4777

World Rank

#5868

Historical Rank

Computational Chemistry

#51

World Rank

#51

Historical Rank

Chemical Engineering

#636

World Rank

#656

Historical Rank

chemistry Degrees

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Chemistry

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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)

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What Schools Are Affiliated With Paolo Carloni?

Paolo Carloni is affiliated with the following schools:

University of California, Berkeley
Curtin University
ETH Zurich
National University of Rosario
Stanford University
RWTH Aachen University
University of Florence
International School for Advanced Studies
University of Cagliari
University of Bologna
Leiden University

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What Schools Are Affiliated With Paolo Carloni?

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