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List of works by Carmay Lim

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

scientific article published in February 2006

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

scientific article

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

scientific article

A simple biophysical model emulates budding yeast chromosome condensation

scientific article published in 2015

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

scientific article

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

scientific article published on 21 September 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.

scientific article

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

scientific article (publication date: June 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.

scientific article

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

scientific article published in March 2009

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

scientific article

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

scientific article

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

scientific article published on May 31, 2011

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

scientific article

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

scientific article published in June 2000

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

scientific article published in May 2010

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

scientific article

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

scientific article published on 01 October 2000

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

scientific article

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

scientific article published in August 2005

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

scientific article

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

scientific article published on 01 January 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

scientific article published on 20 February 2014

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

scientific article published on 24 November 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.

scientific article published on 3 November 2010

Factors controlling the reactivity of zinc finger cores

scientific article published on 16 May 2011

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

scientific article published on 14 June 2016

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

scientific article published in October 2002

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

scientific article published in March 2009

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

scientific article published on 01 February 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

scientific article published on 01 February 2006

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

scientific article published in June 2002

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

scientific article

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

scientific article published on 01 December 2018

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

scientific article

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

scientific article

Free and Bound Therapeutic Lithium in Brain Signaling

scientific article published on 26 September 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.

scientific article published on December 2011

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

scientific article published on May 3, 2012

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

scientific article published on 15 June 2018

How Molecular Size Impacts RMSD Applications in Molecular Dynamics Simulations

scientific article published on 7 March 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

scientific article published on 09 November 2018

Identification of labile Zn sites in drug-target proteins

scientific article published on 11 September 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.

scientific article

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

scientific article published on 30 October 2013

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

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

scientific article

Ion selectivity strategies of sodium channel selectivity filters

scientific article published on 24 October 2014

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

scientific article published on 25 May 2011

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

scientific article published in August 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.

scientific article published in August 2009

Modeling Zn²⁺ release from metallothionein.

scientific article published on 21 August 2014

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

scientific article published on December 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.

scientific article

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

scientific article published on 8 April 2008

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

scientific article

Potassium Versus Sodium Selectivity in Monovalent Ion Channel Selectivity Filters

scientific article published on 01 January 2016

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

scientific article

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

scientific article

Prediction of an anti-IgE binding site on IgE.

scientific article published in June 1998

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

scientific article

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

scientific article

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

scientific article published on 16 August 2013

Quantifying polypeptide conformational space: sensitivity to conformation and ensemble definition

scientific article published on 01 August 2006

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

scientific article published on 24 December 2014

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

scientific article published on 20 September 2019

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

scientific article published on 12 August 2008

Relationship between Enzyme/Substrate Properties and Enzyme Efficiency in Hydrolases

article published in 2015

Selectivity Mechanism of the Voltage-gated Proton Channel, HV1

scientific article

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.

scientific article

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

scientific article

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

scientific article published on 17 February 2016

Structural and Physical Basis for Anti-IgE Therapy

scientific article published on 26 June 2015

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

The IgE gene in primates exhibits extraordinary evolutionary diversity ⬇️

scientific article published on November 10, 2011

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

scientific article published on 08 October 2018

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

scientific article published on 01 November 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

scientific article

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

scientific article published in November 2008

Toward absolute density of states calculations for proteins

scientific article published in June 2006

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

scientific article

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

scientific article

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 ⬇️

scientific article published on March 13, 2012

Zn protein simulations including charge transfer and local polarization effects

scientific article published in April 2005

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