Lista de obras - Carmay Lim - Dominio Público Uruguay

A DFT/CDM Study of metal-carboxylate interactions in metalloproteins: factors governing the maximum number of metal-bound carboxylates

artículo científico publicado en 2006

A combined experimental and theoretical study of divalent metal ion selectivity and function in proteins: application to E. coli ribonuclease H1.

artículo científico publicado en 2003

A fast method for predicting amino acid mutations that lead to unfolding.

artículo científico publicado en 2001

A simple biophysical model emulates budding yeast chromosome condensation

artículo científico publicado en 2015

A structural-alphabet-based strategy for finding structural motifs across protein families.

artículo científico publicado en 2010

All-electron calculations of the nucleation structures in metal-induced zinc-finger folding: role of the Peptide backbone.

artículo científico publicado en 2007

Allosteric coupling between transmembrane segment 4 and the selectivity filter of TALK1 potassium channels regulates their gating by extracellular pH

scientific article published on 29 April 2022

An azido-BODIPY probe for glycosylation: initiation of strong fluorescence upon triazole formation.

artículo científico publicado en 2014

An efficient protocol for computing the pKa of Zn-bound water

scientific article published on 01 December 2018

Arrangement of 3D structural motifs in ribosomal RNA

artículo científico publicado en 2010

Benchmarking polarizable and non-polarizable force fields for Ca2+-peptides against a comprehensive QM dataset

scientific article published on 01 October 2020

Clustangles: An Open Library for Clustering Angular Data.

artículo científico publicado en 2015

Combined experimental and theoretical study of long-range interactions modulating dimerization and activity of yeast geranylgeranyl diphosphate synthase

artículo científico publicado en 2009

Competition among Ca2+, Mg2+, and Na+ for model ion channel selectivity filters: determinants of ion selectivity.

artículo científico publicado en 2012

Competition among metal ions for protein binding sites: determinants of metal ion selectivity in proteins.

artículo científico publicado en 2013

Competition between Li+ and Mg2+ in Metalloproteins. Implications for Lithium Therapy ⬇️

artículo científico publicado el 31 de mayo de 2011

Competition between Li+ and Na+ in sodium transporters and receptors: Which Na+-Binding sites are "therapeutic" Li+ targets?

artículo científico publicado en 2018

Competition between protein ligands and cytoplasmic inorganic anions for the metal cation: a DFT/CDM study

article

Computational studies of the coordination stereochemistry, bonding, and metal selectivity of mercury

scientific article published on 01 January 2006

Conformational analysis of long spacers in PROSITE patterns.

artículo científico publicado en 2000

Conserved structural motif for recognizing nicotinamide adenine dinucleotide in poly(ADP-ribose) polymerases and ADP-ribosylating toxins: implications for structure-based drug design.

artículo científico publicado en 2010

DR_bind: a web server for predicting DNA-binding residues from the protein structure based on electrostatics, evolution and geometry.

artículo científico publicado en 2012

Design, synthesis, and SAR of novel carbapenem antibiotics with high stability to Xanthomonas maltophilia oxyiminocephalosporinase type II

artículo científico publicado en 2000

Determinants of K+ vs Na+ selectivity in potassium channels.

artículo científico publicado en 2009

Differential effects of the Zn-His-Bkb vs Zn-His-[Asp/Glu] triad on Zn-core stability and reactivity

artículo científico publicado en 2005

Discovering structural motifs using a structural alphabet: application to magnesium-binding sites

artículo científico publicado en 2007

Effect of carboxylate-binding mode on metal binding/selectivity and function in proteins

artículo científico publicado en 2007

Empirical force fields for biologically active divalent metal cations in water

scientific article published on 01 January 2006

Evolution of Eukaryotic Ion Channels: Principles Underlying the Conversion of Ca2+-Selective to Na+-Selective Channels

artículo científico publicado en 2014

Factors Governing the Bridging Water Protonation State in Polynuclear Mg(2+) Proteins.

artículo científico publicado en 2015

Factors Governing the Different Functions of Zn2+-Sites with Identical Ligands in Proteins

scientific article published on 11 September 2019

Factors controlling the mechanism of NAD(+) non-redox reactions.

artículo científico publicado en 2010

Factors controlling the reactivity of zinc finger cores

artículo científico publicado en 2011

Factors controlling the selectivity for Na(+) over Mg(2+) in sodium transporters and enzymes.

artículo científico publicado en 2016

Factors governing intrinsic chemical reactivity differences between clavulanic and penicillanic acids.

artículo científico publicado en 2002

Factors governing metal-ligand distances and coordination geometries of metal complexes

artículo científico publicado en 2009

Factors governing the Na(+) vs K(+) selectivity in sodium ion channels

artículo científico publicado en 2010

Factors governing the metal coordination number in isolated group IA and IIA metal hydrates

scientific article published on 01 June 2006

Factors governing the metal coordination number in metal complexes from Cambridge Structural Database analyses

artículo científico publicado en 2006

Factors governing the protonation state of cysteines in proteins: an Ab initio/CDM study.

artículo científico publicado en 2002

Factors governing the substitution of La3+ for Ca2+ and Mg2+ in metalloproteins: a DFT/CDM study

artículo científico publicado en 2005

Factors governing when a metal-bound water is deprotonated in proteins

artículo científico publicado en 2018

First-second shell interactions in metal binding sites in proteins: a PDB survey and DFT/CDM calculations.

artículo científico publicado en 2003

Force fields including charge transfer and local polarization effects: Application to proteins containing multi/heavy metal ions.

artículo científico publicado en 2009

Free and Bound Therapeutic Lithium in Brain Signaling

artículo científico publicado en 2019

Gene Silencing Mechanisms Revealed by Dynamics of Guide, Target, and Duplex Binding to Argonaute

scientific article published on 10 December 2019

GeoPCA: a new tool for multivariate analysis of dihedral angles based on principal component geodesics.

artículo científico publicado en 2011

Hidden Relationship between Conserved Residues and Locally Conserved Phosphate-Binding Structures in NAD(P)-Binding Proteins ⬇️

artículo científico publicado el 3 de mayo de 2012

How First Shell-Second Shell Interactions and Metal Substitution Modulate Protein Function

artículo científico publicado en 2018

How Molecular Size Impacts RMSD Applications in Molecular Dynamics Simulations

artículo científico publicado en 2017

How Native and Non-Native Cations Bind and Modulate the Properties of GTP/ATP

How Pb Binds and Modulates Properties of Ca-Signaling Proteins

artículo científico publicado en 2018

Identification of labile Zn sites in drug-target proteins

artículo científico publicado en 2013

Identifying RNA-binding residues based on evolutionary conserved structural and energetic features

scientific article published on 16 December 2013

Identifying the mechanism of protein loop closure: a molecular dynamics simulation of the Bacillus stearothermophilus LDH loop in solution.

artículo científico publicado en 1995

Importance of metal hydration on the selectivity of Mg2+ versus Ca2+ in magnesium ion channels.

artículo científico publicado en 2013

Internal-state nonequilibrium effects for a fast, second-order reaction

Ion selectivity in the selectivity filters of acid-sensing ion channels

artículo científico publicado en 2015

Ion selectivity strategies of sodium channel selectivity filters

artículo científico publicado en 2014

Linking distinct conformations of nicotinamide adenine dinucleotide with protein fold/function.

artículo científico publicado en 2011

Mechanism of DNA-binding loss upon single-point mutation in p53.

artículo científico publicado en 2007

Metal binding affinity and selectivity in metalloproteins: insights from computational studies.

scientific article published on January 2008

Metal-binding affinity and selectivity of nonstandard natural amino acid residues from DFT/CDM calculations.

artículo científico publicado en 2009

Modeling Zn²⁺ release from metallothionein.

artículo científico publicado en 2014

Molecular dynamics simulation of E. coli ribonuclease H1 in solution: correlation with NMR and X-ray data and insights into biological function.

artículo científico publicado en 1995

Mononuclear versus binuclear metal-binding sites: metal-binding affinity and selectivity from PDB survey and DFT/CDM calculations

scientific article published on 28 February 2008

New techniques for the study of non-equilibrium effects in non-first-order systems

Nonequilibrium effects in chemical kinetics. Straight-line paths for homonuclear diatomic dissociation-recombination process

Oxyanion selectivity in sulfate and molybdate transport proteins: an ab initio/CDM study.

artículo científico publicado en 2004

Physical basis of structural and catalytic Zn-binding sites in proteins

artículo científico publicado en 2008

Polarization-consistent versus correlation-consistent basis sets in predicting molecular and spectroscopic properties.

artículo científico publicado en 2007

Potassium Versus Sodium Selectivity in Monovalent Ion Channel Selectivity Filters

artículo científico publicado en 2016

Predicting DNA-binding amino acid residues from electrostatic stabilization upon mutation to Asp/Glu and evolutionary conservation.

artículo científico publicado en 2007

Predicting RNA-binding sites from the protein structure based on electrostatics, evolution and geometry.

artículo científico publicado en 2008

Prediction of an anti-IgE binding site on IgE.

artículo científico publicado en 1998

Preparing a human membrane and secreted protein-enriched cDNA library using PCR primers derived from a genomic database.

artículo científico publicado en 2001

Principles governing Mg, Ca, and Zn binding and selectivity in proteins.

artículo científico publicado en 2003

Protein-Protein Docking Using EMAP in CHARMM and Support Vector Machine: Application to Ab/Ag Complexes.

artículo científico publicado en 2013

Quantifying polypeptide conformational space: sensitivity to conformation and ensemble definition

artículo científico publicado en 2006

Quantum-chemistry based calibration of the alkali metal cation series (Li+Cs+) for large-scale polarizable molecular mechanics/dynamics simulations

artículo científico publicado en 2014

Ran pathway-independent regulation of mitotic Golgi disassembly by Importin-α

artículo científico publicado en 2019

Reformulation of Maxwell's equations to incorporate near-solute solvent structure

artículo científico publicado en 2008

Relationship between Enzyme/Substrate Properties and Enzyme Efficiency in Hydrolases

article published in 2015

Selectivity Mechanism of the Voltage-gated Proton Channel, HV1

artículo científico publicado en 2015

Sensitivity of Functional Loop Conformations on Long-Range Electrostatics: Implications for M20 Loop Dynamics in E. coli Dihydrofolate Reductase

scientific article published on 24 March 2020

Sequence-motif detection of NAD(P)-binding proteins: discovery of a unique antibacterial drug target.

artículo científico publicado en 2014

Strategies to model the near-solute solvent molecular density/polarization

scientific article published on 01 April 2009

Structural Basis for the Magnesium-Dependent Activation and Hexamerization of the Lon AAA+ Protease

artículo científico publicado en 2016

Structural Characterization of the Phosphotyrosine Binding Region of a High-Affinity SH2 Domain−Phosphopeptide Complex by Molecular Dynamics Simulation and Chemical Shift Calculations

article

Structural analysis of disease-related TDP-43 D169G mutation: linking enhanced stability and caspase cleavage efficiency to protein accumulation

artículo científico publicado en 2016

Structural and Physical Basis for Anti-IgE Therapy

artículo científico publicado en 2015

Study of mixture effects in the nonequilibrium kinetics of homonuclear diatomic dissociation and recombination

The IgE gene in primates exhibits extraordinary evolutionary diversity ⬇️

artículo científico publicado el 10 de noviembre de 2011

The Zinc Linchpin Motif in the DNA Repair Glycosylase MUTYH: Identifying the Zn Ligands and Roles in Damage Recognition and Repair

artículo científico publicado en 2018

The binding mode of an E-64 analog to the active site of cathepsin B

artículo científico publicado en 1996

The double catalytic triad, Cys25-His159-Asp158 and Cys25-His159-Asn175, in papain catalysis: role of Asp158 and Asn175

scientific article published on 01 January 1994

The effect of vibrational-rotational disequilibrium on the rate constant for an atom-transfer reaction

article

The existence of straight‐line paths, invariant vectors, and invariant tensors characterizing nonequilibrium state distributions during chemical reactions

artículo científico

The importance of excluded solvent volume effects in computing hydration free energies

artículo científico publicado en 2008

Toward absolute density of states calculations for proteins

artículo científico publicado en 2006

Two potential therapeutic antibodies bind to a peptide segment of membrane-bound IgE in different conformations

artículo científico publicado en 2014

Using an Old Drug to Target a New Drug Site: Application of Disulfiram to Target the Zn-Site in HCV NS5A Protein.

artículo científico publicado en 2016

Why Cellular Di/Triphosphates Preferably Bind Mg2+ and Not Ca2

scientific article published on 27 November 2019

Why voltage-gated Ca2+ and bacterial Na+ channels with the same EEEE motif in their selectivity filters confer opposite metal selectivity ⬇️

artículo científico publicado el 13 de marzo de 2012

Zn protein simulations including charge transfer and local polarization effects

artículo científico publicado en 2005

Lista de obras de Carmay Lim

A DFT/CDM Study of metal-carboxylate interactions in metalloproteins: factors governing the maximum number of metal-bound carboxylates

A combined experimental and theoretical study of divalent metal ion selectivity and function in proteins: application to E. coli ribonuclease H1.

A fast method for predicting amino acid mutations that lead to unfolding.

A simple biophysical model emulates budding yeast chromosome condensation

A structural-alphabet-based strategy for finding structural motifs across protein families.

All-electron calculations of the nucleation structures in metal-induced zinc-finger folding: role of the Peptide backbone.

Allosteric coupling between transmembrane segment 4 and the selectivity filter of TALK1 potassium channels regulates their gating by extracellular pH

An azido-BODIPY probe for glycosylation: initiation of strong fluorescence upon triazole formation.

An efficient protocol for computing the pKa of Zn-bound water

Arrangement of 3D structural motifs in ribosomal RNA

Benchmarking polarizable and non-polarizable force fields for Ca2+-peptides against a comprehensive QM dataset

Clustangles: An Open Library for Clustering Angular Data.

Combined experimental and theoretical study of long-range interactions modulating dimerization and activity of yeast geranylgeranyl diphosphate synthase

Competition among Ca2+, Mg2+, and Na+ for model ion channel selectivity filters: determinants of ion selectivity.

Competition among metal ions for protein binding sites: determinants of metal ion selectivity in proteins.

Competition between Li+ and Mg2+ in Metalloproteins. Implications for Lithium Therapy ⬇️

Competition between Li+ and Na+ in sodium transporters and receptors: Which Na+-Binding sites are "therapeutic" Li+ targets?

Competition between protein ligands and cytoplasmic inorganic anions for the metal cation: a DFT/CDM study

Computational studies of the coordination stereochemistry, bonding, and metal selectivity of mercury

Conformational analysis of long spacers in PROSITE patterns.

Conserved structural motif for recognizing nicotinamide adenine dinucleotide in poly(ADP-ribose) polymerases and ADP-ribosylating toxins: implications for structure-based drug design.

DR_bind: a web server for predicting DNA-binding residues from the protein structure based on electrostatics, evolution and geometry.

Design, synthesis, and SAR of novel carbapenem antibiotics with high stability to Xanthomonas maltophilia oxyiminocephalosporinase type II

Determinants of K+ vs Na+ selectivity in potassium channels.

Differential effects of the Zn-His-Bkb vs Zn-His-[Asp/Glu] triad on Zn-core stability and reactivity

Discovering structural motifs using a structural alphabet: application to magnesium-binding sites

Effect of carboxylate-binding mode on metal binding/selectivity and function in proteins

Empirical force fields for biologically active divalent metal cations in water

Evolution of Eukaryotic Ion Channels: Principles Underlying the Conversion of Ca2+-Selective to Na+-Selective Channels

Factors Governing the Bridging Water Protonation State in Polynuclear Mg(2+) Proteins.

Factors Governing the Different Functions of Zn2+-Sites with Identical Ligands in Proteins

Factors controlling the mechanism of NAD(+) non-redox reactions.

Factors controlling the reactivity of zinc finger cores

Factors controlling the selectivity for Na(+) over Mg(2+) in sodium transporters and enzymes.

Factors governing intrinsic chemical reactivity differences between clavulanic and penicillanic acids.

Factors governing metal-ligand distances and coordination geometries of metal complexes

Factors governing the Na(+) vs K(+) selectivity in sodium ion channels

Factors governing the metal coordination number in isolated group IA and IIA metal hydrates

Factors governing the metal coordination number in metal complexes from Cambridge Structural Database analyses

Factors governing the protonation state of cysteines in proteins: an Ab initio/CDM study.

Factors governing the substitution of La3+ for Ca2+ and Mg2+ in metalloproteins: a DFT/CDM study

Factors governing when a metal-bound water is deprotonated in proteins

First-second shell interactions in metal binding sites in proteins: a PDB survey and DFT/CDM calculations.

Force fields including charge transfer and local polarization effects: Application to proteins containing multi/heavy metal ions.

Free and Bound Therapeutic Lithium in Brain Signaling

Gene Silencing Mechanisms Revealed by Dynamics of Guide, Target, and Duplex Binding to Argonaute

GeoPCA: a new tool for multivariate analysis of dihedral angles based on principal component geodesics.

Hidden Relationship between Conserved Residues and Locally Conserved Phosphate-Binding Structures in NAD(P)-Binding Proteins ⬇️

How First Shell-Second Shell Interactions and Metal Substitution Modulate Protein Function

How Molecular Size Impacts RMSD Applications in Molecular Dynamics Simulations

How Native and Non-Native Cations Bind and Modulate the Properties of GTP/ATP

How Pb Binds and Modulates Properties of Ca-Signaling Proteins

Identification of labile Zn sites in drug-target proteins

Identifying RNA-binding residues based on evolutionary conserved structural and energetic features

Identifying the mechanism of protein loop closure: a molecular dynamics simulation of the Bacillus stearothermophilus LDH loop in solution.

Importance of metal hydration on the selectivity of Mg2+ versus Ca2+ in magnesium ion channels.

Internal-state nonequilibrium effects for a fast, second-order reaction

Ion selectivity in the selectivity filters of acid-sensing ion channels

Ion selectivity strategies of sodium channel selectivity filters

Linking distinct conformations of nicotinamide adenine dinucleotide with protein fold/function.

Mechanism of DNA-binding loss upon single-point mutation in p53.

Metal binding affinity and selectivity in metalloproteins: insights from computational studies.

Metal-binding affinity and selectivity of nonstandard natural amino acid residues from DFT/CDM calculations.

Modeling Zn²⁺ release from metallothionein.

Molecular dynamics simulation of E. coli ribonuclease H1 in solution: correlation with NMR and X-ray data and insights into biological function.

Mononuclear versus binuclear metal-binding sites: metal-binding affinity and selectivity from PDB survey and DFT/CDM calculations

New techniques for the study of non-equilibrium effects in non-first-order systems

Nonequilibrium effects in chemical kinetics. Straight-line paths for homonuclear diatomic dissociation-recombination process

Oxyanion selectivity in sulfate and molybdate transport proteins: an ab initio/CDM study.

Physical basis of structural and catalytic Zn-binding sites in proteins

Polarization-consistent versus correlation-consistent basis sets in predicting molecular and spectroscopic properties.

Potassium Versus Sodium Selectivity in Monovalent Ion Channel Selectivity Filters

Predicting DNA-binding amino acid residues from electrostatic stabilization upon mutation to Asp/Glu and evolutionary conservation.

Predicting RNA-binding sites from the protein structure based on electrostatics, evolution and geometry.

Prediction of an anti-IgE binding site on IgE.

Preparing a human membrane and secreted protein-enriched cDNA library using PCR primers derived from a genomic database.

Principles governing Mg, Ca, and Zn binding and selectivity in proteins.

Protein-Protein Docking Using EMAP in CHARMM and Support Vector Machine: Application to Ab/Ag Complexes.

Quantifying polypeptide conformational space: sensitivity to conformation and ensemble definition