Novel method for probing the specificity binding profile of ligands: applications to HIV protease (Q36344445)

13 August 2017

Novel method for probing the specificity binding profile of ligands: applications to HIV protease (English)

1 reference

13 August 2017

Woody Sherman

1

1 reference

PMCID

3480184

13 August 2017

Bruce Tidor

series ordinal

2

1 reference

13 August 2017

31 March 2008

1 reference

Chemical Biology and Drug Design

13 August 2017

1 reference

13 August 2017

71

1 reference

13 August 2017

5

1 reference

13 August 2017

387-407

1 reference

Mechanisms of drug inhibition of signalling molecules

13 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

Affinity enhancement of an in vivo matured therapeutic antibody using structure-based computational design

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

Cell-signalling dynamics in time and space

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

Novel procedure for modeling ligand/receptor induced fit effects.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

Specificity versus stability in computational protein design

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

Design and synthesis of new templates derived from pyrrolopyrimidine as selective multidrug-resistance-associated protein inhibitors in multidrug resistance

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

Studies on pyrrolopyrimidines as selective inhibitors of multidrug-resistance-associated protein in multidrug resistance

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

Structure of the multidrug resistance efflux transporter EmrE from Escherichia coli

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

Drug resistance in HIV-1 protease: Flexibility-assisted mechanism of compensatory mutations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

Protein flexibility and drug design: how to hit a moving target.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

A history of pepsin and related enzymes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

Evolution of primary protease inhibitor resistance mutations during protease inhibitor salvage therapy

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

Emergence of resistance to protease inhibitor amprenavir in human immunodeficiency virus type 1-infected patients: selection of four alternative viral protease genotypes and influence of viral susceptibility to coadministered reverse transcriptase n

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

Designing non-peptide peptidomimetics in the 21st century: inhibitors targeting conformational ensembles.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

Lack of synergy for inhibitors targeting a multi-drug-resistant HIV-1 protease

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

Computational study of protein specificity: the molecular basis of HIV-1 protease drug resistance

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

Systematic genetic analysis with ordered arrays of yeast deletion mutants

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

Analysis of crystal structures of aspartic proteinases: on the role of amino acid residues adjacent to the catalytic site of pepsin-like enzymes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

Clinically relevant sequence-based genotyping of HBV, HCV, CMV, and HIV.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

Principles for the buffering of genetic variation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

Curling of flap tips in HIV-1 protease as a mechanism for substrate entry and tolerance of drug resistance

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

How does a symmetric dimer recognize an asymmetric substrate? A substrate complex of HIV-1 protease

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

Targeting the HIV-protease in AIDS therapy: a current clinical perspective

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

From molecular to modular cell biology

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

Replicative fitness of protease inhibitor-resistant mutants of human immunodeficiency virus type 1.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

Inhibitors of HIV-1 protease: a major success of structure-assisted drug design

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

Structure-based design of HIV protease inhibitors: sulfonamide-containing 5,6-dihydro-4-hydroxy-2-pyrones as non-peptidic inhibitors

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

Crystal structures of native and inhibited forms of human cathepsin D: implications for lysosomal targeting and drug design

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

Crystal structure of human pepsin and its complex with pepstatin

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

Solvent-accessible surfaces of proteins and nucleic acids

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

The protein kinase family: conserved features and deduced phylogeny of the catalytic domains

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

Crystallographic analysis of a complex between human immunodeficiency virus type 1 protease and acetyl-pepstatin at 2.0-A resolution

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

Electrostatic interactions in macromolecules: theory and applications

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

The Protein Data Bank: a computer-based archival file for macromolecular structures

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

Kinetic properties of saquinavir-resistant mutants of human immunodeficiency virus type 1 protease and their implications in drug resistance in vivo

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

Mutational anatomy of an HIV-1 protease variant conferring cross-resistance to protease inhibitors in clinical trials. Compensatory modulations of binding and activity

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

Kinetic characterization and cross-resistance patterns of HIV-1 protease mutants selected under drug pressure

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

In vivo and in vitro autoprocessing of human immunodeficiency virus protease expressed in Escherichia coli

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

Human immunodeficiency virus protease. Bacterial expression and characterization of the purified aspartic protease

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480184

Functional classification of drugs by properties of their pairwise interactions.

29 June 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1747-0285.2008.00659.X

Rational cytokine design for increased lifetime and enhanced potency using pH-activated "histidine switching".

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1747-0285.2008.00659.X

Predicting molecular interactions and inducible complementarity: fragment docking of Fab-peptide complexes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1747-0285.2008.00659.X

Ligand-protein inverse docking and its potential use in the computer search of protein targets of a small molecule

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1747-0285.2008.00659.X

Automated design of specificity in molecular recognition

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1747-0285.2008.00659.X

Optimal charges in lead progression: a structure-based neuraminidase case study.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1747-0285.2008.00659.X

Crystal structure and functional analysis of the SurE protein identify a novel phosphatase family

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1747-0285.2008.00659.X

Optimization and computational evaluation of a series of potential active site inhibitors of the V82F/I84V drug-resistant mutant of HIV-1 protease: an application of the relaxed complex method of structure-based drug design

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1747-0285.2008.00659.X

Antiretroviral drug resistance testing in adult HIV-1 infection: recommendations of an International AIDS Society-USA Panel.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1747-0285.2008.00659.X

Statistical potentials for fold assessment.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1747-0285.2008.00659.X

Comparative evaluation of MMPBSA and XSCORE to compute binding free energy in XIAP-peptide complexes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1747-0285.2008.00659.X

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1747-0285.2008.00659.X

Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1747-0285.2008.00659.X

Mechanism of inhibition of pepsin by pepstatin. Effect of inhibitor structure on dissociation constant and time-dependent inhibition

21 January 2018

1 reference

12 December 2020

Accurate prediction of the relative potencies of members of a series of kinase inhibitors using molecular docking and MM-GBSA scoring

1 reference

12 December 2020

Barstar is electrostatically optimized for tight binding to barnase

1 reference

12 December 2020

Designing drugs against heterogeneous targets

1 reference

12 December 2020

Relation between sequence and structure of HIV-1 protease inhibitor complexes: a model system for the analysis of protein flexibility

1 reference

12 December 2020

Charge optimization leads to favorable electrostatic binding free energy

1 reference

12 December 2020

Thermodynamic contributions of the ordered water molecule in HIV-1 protease

1 reference

12 December 2020

10.1111/J.1747-0285.2008.00659.X

Identifiers

DOI

1 reference

13 August 2017

1 reference

13 August 2017

1 reference

PMCID

3480184