List of works - Marc C Nicklaus

A new approach to radial basis function approximation and its application to QSAR.

scientific article published on 28 February 2014

Acylsulfonamide-containing PTP1B inhibitors designed to mimic an enzyme-bound water of hydration

scientific article published in September 2003

Adenosine deaminase prefers a distinct sugar ring conformation for binding and catalysis: kinetic and structural studies

scientific article published in March 2000

An optimized protein kinase C activating diacylglycerol combining high binding affinity (Ki) with reduced lipophilicity (log P).

scientific article published in June 2001

Antiretroviral agents as inhibitors of both human immunodeficiency virus type 1 integrase and protease.

scientific article published on June 1996

Application of azide-alkyne cycloaddition 'click chemistry' for the synthesis of Grb2 SH2 domain-binding macrocycles

scientific article

Authentic HIV-1 Integrase Inhibitors ⬇️

scientific article published on July 1, 2010

Biotinylated biphenyl ketone-containing 2,4-dioxobutanoic acids designed as HIV-1 integrase photoaffinity ligands

scientific article published on 26 September 2006

CERAPP: Collaborative Estrogen Receptor Activity Prediction Project

scientific article published in July 2016

Characterizing the Covalent Targets of a Small Molecule Inhibitor of the Lysine Acetyltransferase P300.

scientific article published on 31 October 2015

Combining docking with pharmacophore filtering for improved virtual screening

scientific article (publication date: 20 May 2009)

Comparison of nine programs predicting pK(a) values of pharmaceutical substances

scientific article published on 01 December 2009

Comparison of the NCI open database with seven large chemical structural databases.

scientific article published in May 2001

Computational chemistry on commodity-type computers

scientific article published in September 1998

Computational tools and resources for metabolism-related property predictions. 1. Overview of publicly available (free and commercial) databases and software

scientific article (publication date: October 2012)

Computational tools and resources for metabolism-related property predictions. 2. Application to prediction of half-life time in human liver microsomes

scientific article

Computer tools in the discovery of HIV-1 integrase inhibitors

scientific article

Computer-aided design and discovery of protein-protein interaction inhibitors as agents for anti-HIV therapy

scientific article published on 9 April 2014

Conformational changes of small molecules binding to proteins

scientific article published on 01 April 1995

Conformational energy range of ligands in protein crystal structures: The difficult quest for accurate understanding

scientific article

Conformationally constrained analogues of diacylglycerol (DAG). 23. Hydrophobic ligand-protein interactions versus ligand-lipid interactions of DAG-lactones with protein kinase C (PK-C).

scientific article published in September 2004

Conformationally constrained analogues of diacylglycerol (DAG). 25. Exploration of the sn-1 and sn-2 carbonyl functionality reveals the essential role of the sn-1 carbonyl at the lipid interface in the binding of DAG-lactones to protein kinase C

scientific article published on September 2005

Conformationally constrained analogues of diacylglycerol. 18. The incorporation of a hydroxamate moiety into diacylglycerol-lactones reduces lipophilicity and helps discriminate between sn-1 and sn-2 binding modes to protein kinase C (PK-C). Implica

scientific article published in December 2001

Conformationally locked nucleoside analogues. Synthesis of dideoxycarbocyclic nucleoside analogues structurally related to neplanocin C

scientific article published on 01 September 1994

Conformationally restricted nucleosides. The reaction of adenosine deaminase with substrates built on a bicyclo[3.1.0]hexane template

scientific article published on 01 April 1999

Corrigendum to “Inhibitors of human tyrosyl-DNA phospodiesterase (hTdp1) developed by virtual screening using ligand-based pharmacophores” [Bioorg. Med. Chem. 18 (2010) 182–189]

scientific article published on 01 March 2010

Depsides and depsidones as inhibitors of HIV-1 integrase: discovery of novel inhibitors through 3D database searching.

scientific article

Design and synthesis of conformationally constrained Grb2 SH2 domain binding peptides employing alpha-methylphenylalanyl based phosphotyrosyl mimetics

scientific article published in February 2005

Differential binding modes of diacylglycerol (DAG) and DAG lactones to protein kinase C (PK-C).

scientific article published in April 2003

Discovery of HIV-1 integrase inhibitors by pharmacophore searching.

scientific article published on March 1997

Discovery of a novel hybrid from finasteride and epristeride as 5α-reductase inhibitor

scientific article published on 28 October 2010

Discovery of novel, non-peptide HIV-1 protease inhibitors by pharmacophore searching.

scientific article published on May 1996

Discovery of thioether-bridged cyclic pentapeptides binding to Grb2-SH2 domain with high affinity

scientific article

Effects of Tyrphostins, Protein Kinase Inhibitors, on Human Immunodeficiency Virus Type 1 Integrase ⬇️

scientific article published on November 21, 1995

Enumeration of ring-chain tautomers based on SMIRKS rules

scientific article

Evaluation of macrocyclic Grb2 SH2 domain-binding peptide mimetics prepared by ring-closing metathesis of C-terminal allylglycines with an N-terminal beta-vinyl-substituted phosphotyrosyl mimetic

scientific article

Evidence that sequence homologous region in LRAT-like proteins possesses anti-proliferative activity and DNA binding properties: translational implications and mechanism of action

scientific article published on 18 October 2005

Examination of acylated 4-aminopiperidine-4-carboxylic acid residues in the phosphotyrosyl+1 position of Grb2 SH2 domain-binding tripeptides

scientific article

Excitations, optical absorption spectra, and optical excitonic gaps of heterofullerenes. I. C60, C59N+, and C48N12: theory and experiment

scientific article published in March 2004

Experimental and Chemoinformatics Study of Tautomerism in a Database of Commercially Available Screening Samples

scientific article (publication date: 28 November 2016)

Experimental and structural evidence that herpes 1 kinase and cellular DNA polymerase(s) discriminate on the basis of sugar pucker

scientific article published on January 2004

Exploration of Ultralarge Compound Collections for Drug Discovery

scientific article published on 14 April 2022

Exploring Potential Binding Modes of Small Drug-like Molecules to the Polo-Box Domain of Human Polo-like Kinase 1.

scientific article

How to Achieve Better Results Using PASS-Based Virtual Screening: Case Study for Kinase Inhibitors

scientific article

Identification of HIV-1 integrase inhibitors via three-dimensional database searching using ASV and HIV-1 integrases as targets.

scientific article published on October 2000

Identification of Shc Src homology 2 domain-binding peptoid-peptide hybrids

scientific article

Inhibition of (cytosine C5)-methyltransferase by oligonucleotides containing flexible (cyclopentane) and conformationally constrained (bicyclo[3.1.0]hexane) abasic sites.

scientific article

Inhibitors for the hepatitis C virus RNA polymerase explored by SAR with advanced machine learning methods.

scientific article published on 29 March 2013

Inhibitors of human tyrosyl-DNA phospodiesterase (hTdp1) developed by virtual screening using ligand-based pharmacophores

scientific article

Interactions of conformationally biased north and south 2'-fluoro-2', 3'-dideoxynucleoside 5'-triphosphates with the active site of HIV-1 reverse transcriptase.

scientific article published in September 2000

Internet resources integrating many small-molecule databases.

scientific article published on January 2008

Macrophilone A: Structure Elucidation, Total Synthesis, and Functional Evaluation of a Biologically Active Iminoquinone from the Marine Hydroid Macrorhynchia philippina

scientific article published on 27 March 2017

Mass spectrometric analysis of the HIV-1 integrase-pyridoxal 5'-phosphate complex reveals a new binding site for a nucleotide inhibitor.

scientific article

Metabolic Regulation of Histone Acetyltransferases by Endogenous Acyl-CoA Cofactors

scientific article

Metal-dependent inhibition of HIV-1 integrase by beta-diketo acids and resistance of the soluble double-mutant (F185K/C280S).

scientific article published in September 2003

Model of full-length HIV-1 integrase complexed with viral DNA as template for anti-HIV drug design.

scientific article

Molecular modeling in the discovery of drug leads

scientific article published on 01 July 1996

Mutation of a conserved serine residue in a quinolone-resistant type II topoisomerase alters the enzyme-DNA and drug interactions.

scientific article published in March 1999

National Cancer Institute Drug Information System 3D database.

scientific article published in September 1994

Novel HIV-1 Integrase Inhibitor Development by Virtual Screening Based on QSAR Models

scientific article published on 13 August 2015

Optical structure recognition software to recover chemical information: OSRA, an open source solution

scientific article

Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop

scientific article

PASS biological activity spectrum predictions in the enhanced open NCI database browser

scientific article published on January 2003

PDB ligand conformational energies calculated quantum-mechanically

scientific article published on 21 February 2012

PROSIT: pseudo-rotational online service and interactive tool, applied to a conformational survey of nucleosides and nucleotides.

scientific article

Pharmacophores in Drug Design and Discovery ⬇️

scientific article published on January 1, 1998

Polo-box domain: a versatile mediator of polo-like kinase function

scientific article

Potent Grb2-SH2 domain antagonists not relying on phosphotyrosine mimics

scientific article

Probing the hras-1Y i-motif with small molecules

scientific article published on 05 October 2018

Prosit, an online service to calculate pseudorotational parameters of nucleosides and nucleotides

scientific article

Protein kinase C. Modeling of the binding site and prediction of binding constants

scientific article published on 01 April 1994

QSAR Modeling Using Large-Scale Databases: Case Study for HIV-1 Reverse Transcriptase Inhibitors

scientific article published on 29 June 2015

QSAR modeling of imbalanced high-throughput screening data in PubChem

scientific article

QSAR of conformationally flexible molecules: comparative molecular field analysis of protein-tyrosine kinase inhibitors

scientific article published on 01 October 1992

ReactionCode: format for reaction searching, analysis, classification, transform, and encoding/decoding

scientific article published on 03 December 2020

SAVI, in silico generation of billions of easily synthesizable compounds through expert-system type rules

scientific article published on 11 November 2020

Sagnac experiment with electrons: Observation of the rotational phase shift of electron waves in vacuum

scientific article published on 01 July 1993

Sculpting the bicyclo[3.1.0]hexane template of carbocyclic nucleosides to improve recognition by herpes thymidine kinase

scientific article published on 24 April 2007

Small nonphosphorylated Grb2-SH2 domain antagonists evaluated by surface plasmon resonance technology

scientific article published in January 2005

Software and resources for computational medicinal chemistry

scientific article (publication date: June 2011)

Structural and functional analyses of minimal phosphopeptides targeting the polo-box domain of polo-like kinase 1

scientific article

Structural basis for a non-phosphorus-containing cyclic peptide binding to Grb2-SH2 domain with high affinity

scientific article published in August 2003

Structure activity of 3-aryl-1,3-diketo-containing compounds as HIV-1 integrase inhibitors.

scientific article published on July 2002

Structure, stability, and NMR properties of lower fullerenes C38-C50 and azafullerene C44N6

scientific article published on 01 May 2005

Structure-based design of potent Grb2-SH2 domain antagonists not relying on phosphotyrosine mimics

scientific article published on 22 August 2006

Structure-based design of thioether-bridged cyclic phosphopeptides binding to Grb2-SH2 domain

scientific article

Synthesis and conformational analysis of a locked analogue of carbovir built on a bicyclo[3.1.0]hex-2-enyl template

scientific article

Synthesis, anti-cancer screening and tyrosyl-DNA phosphodiesterase 1 (Tdp1) inhibition activity of novel piperidinyl sulfamides

scientific article published on 13 October 2017

Tautomer Database: A Comprehensive Resource for Tautomerism Analyses

scientific article published on 10 March 2020

Tautomerism and magnesium chelation of HIV-1 integrase inhibitors: a theoretical study.

scientific article

Tautomerism of Warfarin: Combined Chemoinformatics, Quantum Chemical, and NMR Investigation

scientific article published on 25 September 2015

Therapeutic Antibodies to Ganglioside GD2 Evolved from Highly Selective Germline Antibodies.

scientific article published in August 2017

Total synthesis and biological evaluation of largazole and derivatives with promising selectivity for cancers cells

scientific article

Toward a Comprehensive Treatment of Tautomerism in Chemoinformatics Including in InChI V2

scientific article published on 10 March 2020

Use of computer graphics in drug design.

scientific article published on January 1993

Utilization of a common pathway for the synthesis of high affinity macrocyclic Grb2 SH2 domain-binding peptide mimetics that differ in the configuration at one ring junction

scientific article published on 01 April 2005

Utilization of a nitrobenzoxadiazole (NBD) fluorophore in the design of a Grb2 SH2 domain-binding peptide mimetic

scientific article published in March 2005

Virtual screening application of a model of full-length HIV-1 integrase complexed with viral DNA

scientific article published on 11 August 2007

Virtual screening using ligand-based pharmacophores for inhibitors of human tyrosyl-DNA phospodiesterase (hTdp1)

scientific article published on 02 March 2010

Wien filter: A wave-packet-shifting device for restoring longitudinal coherence in charged-matter-wave interferometers

[Discovering new antiretroviral compounds in "Big Data" chemical space of the SAVI library]

scientific article published on 01 February 2019

List of works by Marc C Nicklaus

A new approach to radial basis function approximation and its application to QSAR.

Acylsulfonamide-containing PTP1B inhibitors designed to mimic an enzyme-bound water of hydration

Adenosine deaminase prefers a distinct sugar ring conformation for binding and catalysis: kinetic and structural studies

An optimized protein kinase C activating diacylglycerol combining high binding affinity (Ki) with reduced lipophilicity (log P).

Antiretroviral agents as inhibitors of both human immunodeficiency virus type 1 integrase and protease.

Application of azide-alkyne cycloaddition 'click chemistry' for the synthesis of Grb2 SH2 domain-binding macrocycles

Authentic HIV-1 Integrase Inhibitors ⬇️

Biotinylated biphenyl ketone-containing 2,4-dioxobutanoic acids designed as HIV-1 integrase photoaffinity ligands

CERAPP: Collaborative Estrogen Receptor Activity Prediction Project

Characterizing the Covalent Targets of a Small Molecule Inhibitor of the Lysine Acetyltransferase P300.

Combining docking with pharmacophore filtering for improved virtual screening

Comparison of nine programs predicting pK(a) values of pharmaceutical substances

Comparison of the NCI open database with seven large chemical structural databases.

Computational chemistry on commodity-type computers

Computational tools and resources for metabolism-related property predictions. 1. Overview of publicly available (free and commercial) databases and software

Computational tools and resources for metabolism-related property predictions. 2. Application to prediction of half-life time in human liver microsomes

Computer tools in the discovery of HIV-1 integrase inhibitors

Computer-aided design and discovery of protein-protein interaction inhibitors as agents for anti-HIV therapy

Conformational changes of small molecules binding to proteins

Conformational energy range of ligands in protein crystal structures: The difficult quest for accurate understanding

Conformationally constrained analogues of diacylglycerol (DAG). 23. Hydrophobic ligand-protein interactions versus ligand-lipid interactions of DAG-lactones with protein kinase C (PK-C).

Conformationally constrained analogues of diacylglycerol (DAG). 25. Exploration of the sn-1 and sn-2 carbonyl functionality reveals the essential role of the sn-1 carbonyl at the lipid interface in the binding of DAG-lactones to protein kinase C

Conformationally constrained analogues of diacylglycerol. 18. The incorporation of a hydroxamate moiety into diacylglycerol-lactones reduces lipophilicity and helps discriminate between sn-1 and sn-2 binding modes to protein kinase C (PK-C). Implica

Conformationally locked nucleoside analogues. Synthesis of dideoxycarbocyclic nucleoside analogues structurally related to neplanocin C

Conformationally restricted nucleosides. The reaction of adenosine deaminase with substrates built on a bicyclo[3.1.0]hexane template

Corrigendum to “Inhibitors of human tyrosyl-DNA phospodiesterase (hTdp1) developed by virtual screening using ligand-based pharmacophores” [Bioorg. Med. Chem. 18 (2010) 182–189]

Depsides and depsidones as inhibitors of HIV-1 integrase: discovery of novel inhibitors through 3D database searching.

Design and synthesis of conformationally constrained Grb2 SH2 domain binding peptides employing alpha-methylphenylalanyl based phosphotyrosyl mimetics

Differential binding modes of diacylglycerol (DAG) and DAG lactones to protein kinase C (PK-C).

Discovery of HIV-1 integrase inhibitors by pharmacophore searching.

Discovery of a novel hybrid from finasteride and epristeride as 5α-reductase inhibitor

Discovery of novel, non-peptide HIV-1 protease inhibitors by pharmacophore searching.

Discovery of thioether-bridged cyclic pentapeptides binding to Grb2-SH2 domain with high affinity

Effects of Tyrphostins, Protein Kinase Inhibitors, on Human Immunodeficiency Virus Type 1 Integrase ⬇️

Enumeration of ring-chain tautomers based on SMIRKS rules

Evaluation of macrocyclic Grb2 SH2 domain-binding peptide mimetics prepared by ring-closing metathesis of C-terminal allylglycines with an N-terminal beta-vinyl-substituted phosphotyrosyl mimetic

Evidence that sequence homologous region in LRAT-like proteins possesses anti-proliferative activity and DNA binding properties: translational implications and mechanism of action

Examination of acylated 4-aminopiperidine-4-carboxylic acid residues in the phosphotyrosyl+1 position of Grb2 SH2 domain-binding tripeptides

Excitations, optical absorption spectra, and optical excitonic gaps of heterofullerenes. I. C60, C59N+, and C48N12: theory and experiment

Experimental and Chemoinformatics Study of Tautomerism in a Database of Commercially Available Screening Samples

Experimental and structural evidence that herpes 1 kinase and cellular DNA polymerase(s) discriminate on the basis of sugar pucker

Exploration of Ultralarge Compound Collections for Drug Discovery

Exploring Potential Binding Modes of Small Drug-like Molecules to the Polo-Box Domain of Human Polo-like Kinase 1.

How to Achieve Better Results Using PASS-Based Virtual Screening: Case Study for Kinase Inhibitors

Identification of HIV-1 integrase inhibitors via three-dimensional database searching using ASV and HIV-1 integrases as targets.

Identification of Shc Src homology 2 domain-binding peptoid-peptide hybrids

Inhibition of (cytosine C5)-methyltransferase by oligonucleotides containing flexible (cyclopentane) and conformationally constrained (bicyclo[3.1.0]hexane) abasic sites.

Inhibitors for the hepatitis C virus RNA polymerase explored by SAR with advanced machine learning methods.

Inhibitors of human tyrosyl-DNA phospodiesterase (hTdp1) developed by virtual screening using ligand-based pharmacophores

Interactions of conformationally biased north and south 2'-fluoro-2', 3'-dideoxynucleoside 5'-triphosphates with the active site of HIV-1 reverse transcriptase.

Internet resources integrating many small-molecule databases.

Macrophilone A: Structure Elucidation, Total Synthesis, and Functional Evaluation of a Biologically Active Iminoquinone from the Marine Hydroid Macrorhynchia philippina

Mass spectrometric analysis of the HIV-1 integrase-pyridoxal 5'-phosphate complex reveals a new binding site for a nucleotide inhibitor.

Metabolic Regulation of Histone Acetyltransferases by Endogenous Acyl-CoA Cofactors

Metal-dependent inhibition of HIV-1 integrase by beta-diketo acids and resistance of the soluble double-mutant (F185K/C280S).

Model of full-length HIV-1 integrase complexed with viral DNA as template for anti-HIV drug design.

Molecular modeling in the discovery of drug leads

Mutation of a conserved serine residue in a quinolone-resistant type II topoisomerase alters the enzyme-DNA and drug interactions.

National Cancer Institute Drug Information System 3D database.

Novel HIV-1 Integrase Inhibitor Development by Virtual Screening Based on QSAR Models

Optical structure recognition software to recover chemical information: OSRA, an open source solution

Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop

PASS biological activity spectrum predictions in the enhanced open NCI database browser

PDB ligand conformational energies calculated quantum-mechanically

PROSIT: pseudo-rotational online service and interactive tool, applied to a conformational survey of nucleosides and nucleotides.

Pharmacophores in Drug Design and Discovery ⬇️

Polo-box domain: a versatile mediator of polo-like kinase function

Potent Grb2-SH2 domain antagonists not relying on phosphotyrosine mimics

Probing the hras-1Y i-motif with small molecules

Prosit, an online service to calculate pseudorotational parameters of nucleosides and nucleotides

Protein kinase C. Modeling of the binding site and prediction of binding constants

QSAR Modeling Using Large-Scale Databases: Case Study for HIV-1 Reverse Transcriptase Inhibitors

QSAR modeling of imbalanced high-throughput screening data in PubChem

QSAR of conformationally flexible molecules: comparative molecular field analysis of protein-tyrosine kinase inhibitors

ReactionCode: format for reaction searching, analysis, classification, transform, and encoding/decoding

SAVI, in silico generation of billions of easily synthesizable compounds through expert-system type rules

Sagnac experiment with electrons: Observation of the rotational phase shift of electron waves in vacuum

Sculpting the bicyclo[3.1.0]hexane template of carbocyclic nucleosides to improve recognition by herpes thymidine kinase

Small nonphosphorylated Grb2-SH2 domain antagonists evaluated by surface plasmon resonance technology