In silico fragment-based drug design (Q38029118)

27 August 2017

In silico fragment-based drug design (English)

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27 August 2017

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Zenon D Konteatis

1

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PubMed ID

22827744

27 August 2017

language of work or name

English

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publication date

8 October 2010

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Expert Opinion on Drug Discovery

27 August 2017

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27 August 2017

5

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27 August 2017

11

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27 August 2017

1047-1065

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Rational design of peptide-based HIV proteinase inhibitors

27 August 2017

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Design, activity, and 2.8 A crystal structure of a C2 symmetric inhibitor complexed to HIV-1 protease

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2010.523697

L-735,524: the design of a potent and orally bioavailable HIV protease inhibitor

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Integrating virtual screening in lead discovery

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Virtual screening of chemical libraries

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Molecular Shape and Medicinal Chemistry: A Perspective

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

An analysis of the binding efficiencies of drugs and their leads in successful drug discovery programs

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2010.523697

The process of structure-based drug design

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

On the attribution and additivity of binding energies

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Discovering high-affinity ligands for proteins: SAR by NMR

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Fragment-based screening using X-ray crystallography and NMR spectroscopy

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

SAR by MS: a ligand based technique for drug lead discovery against structured RNA targets

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Fragment-based screening using surface plasmon resonance technology

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Tethering: fragment-based drug discovery

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Identification of inhibitors of checkpoint kinase 1 through template screening

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

A decade of fragment-based drug design: strategic advances and lessons learned

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Advances in fragment-based drug discovery platforms

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Recent developments in fragment-based drug discovery

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Fragment-based drug discovery: what has it achieved so far?

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

From fragment to clinical candidate--a historical perspective.

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Components of successful lead generation

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Novel inhibitors of DNA gyrase: 3D structure based biased needle screening, hit validation by biophysical methods, and 3D guided optimization. A promising alternative to random screening

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Application of fragment-based lead generation to the discovery of novel, cyclic amidine beta-secretase inhibitors with nanomolar potency, cellular activity, and high ligand efficiency

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

High-throughput drug discovery: what can we expect from HTS?

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

The art and practice of structure-based drug design: A molecular modeling perspective

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Molecular complexity and its impact on the probability of finding leads for drug discovery

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Library design for fragment based screening

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

21 January 2018

NMR in drug discovery

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

The genesis of high-throughput structure-based drug discovery using protein crystallography

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

High-throughput crystallography for lead discovery in drug design.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2010.523697

The maximal affinity of ligands

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Ligand efficiency: a useful metric for lead selection

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Ligand efficiency indices as guideposts for drug discovery.

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

The role of molecular size in ligand efficiency

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Ligand efficiency indices for effective drug discovery

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

The influence of drug-like concepts on decision-making in medicinal chemistry

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Do enthalpy and entropy distinguish first in class from best in class?

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Fragment-based lead discovery

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Hydrogen bonding and biological specificity analysed by protein engineering

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Application and limitations of X-ray crystallographic data in structure-based ligand and drug design

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Astex, Structural Genomix, and Syrrx

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

High-throughput crystallography to enhance drug discovery

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Locating and characterizing binding sites on proteins

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Proteins in organic solvents

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Derivation of rules for comparative protein modeling from a database of protein structure alignments

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Evaluation of comparative protein modeling by MODELLER

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Homology modeling by the ICM method

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Kinases, Homology Models, and High Throughput Docking

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Utility of homology models in the drug discovery process.

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

BCR-ABL alternative splicing as a common mechanism for imatinib resistance: evidence from molecular dynamics simulations

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Modeling and selection of flexible proteins for structure-based drug design: backbone and side chain movements in p38 MAPK.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Type-II kinase inhibitor docking, screening, and profiling using modified structures of active kinase states

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2010.523697

An antibody against DR4 (TRAIL-R1) in combination with doxorubicin selectively kills malignant but not normal prostate cells.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Dissecting physiological roles of estrogen receptor alpha and beta with potent selective ligands from structure-based design

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2010.523697

A comparative study of available software for high-accuracy homology modeling: from sequence alignments to structural models

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Cost of innovation in the pharmaceutical industry

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

The price of innovation: new estimates of drug development costs

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Molecular properties that influence the oral bioavailability of drug candidates

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

A ‘Rule of Three’ for fragment-based lead discovery?

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Library design for NMR-based screening

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Design of small molecule libraries for NMR screening and other applications in drug discovery

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Integration of fragment screening and library design

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Characteristic physical properties and structural fragments of marketed oral drugs.

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Theory and applications of NMR-based screening in pharmaceutical research

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

RECAP--retrosynthetic combinatorial analysis procedure: a powerful new technique for identifying privileged molecular fragments with useful applications in combinatorial chemistry

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

The many roles of computation in drug discovery

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Computer-based de novo design of drug-like molecules

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Docking, virtual high throughput screening and in silico fragment-based drug design

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

The statistical-thermodynamic basis for computation of binding affinities: a critical review

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Ligand affinities predicted with the MM/PBSA method: dependence on the simulation method and the force field.

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Grand canonical Monte Carlo simulation of ligand-protein binding.

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Grand canonical free-energy calculations of protein-ligand binding.

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Fragment-based computation of binding free energies by systematic sampling.

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Functionality maps of binding sites: a multiple copy simultaneous search method

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

HOOK: a program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding site

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

The computer program LUDI: a new method for the de novo design of enzyme inhibitors

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2010.523697

PRO-LIGAND: an approach to de novo molecular design. 1. Application to the design of organic molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2010.523697

LigBuilder: A Multi-Purpose Program for Structure-Based Drug Design

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Protein-ligand docking: current status and future challenges

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go.

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

A geometric approach to macromolecule-ligand interactions

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Recent advances in de novo design strategy for practical lead identification

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

A critical assessment of docking programs and scoring functions

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Predicting protein druggability

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Identifying and characterizing binding sites and assessing druggability

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Druggability indices for protein targets derived from NMR-based screening data

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Structure-based maximal affinity model predicts small-molecule druggability.

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Understanding and predicting druggability. A high-throughput method for detection of drug binding sites

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Identification of hot spots within druggable binding regions by computational solvent mapping of proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Binding site detection and druggability index from first principles.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Combinatorial docking and combinatorial chemistry: design of potent non-peptide thrombin inhibitors

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2010.523697

The reversed binding of beta-phenethylamine inhibitors of DPP-IV: X-ray structures and properties of novel fragment and elaborated inhibitors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Pyrazole urea-based inhibitors of p38 MAP kinase: from lead compound to clinical candidate

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Molecular docking and ligand specificity in fragment-based inhibitor discovery

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Scoring of KDR kinase inhibitors: using interaction energy as a guide for ranking

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Novel procedure for modeling ligand/receptor induced fit effects.

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Tackling the challenges posed by target flexibility in drug design

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Principles of protein-protein interactions

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Targeting protein-protein interactions for cancer therapy

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Reaching for high-hanging fruit in drug discovery at protein-protein interfaces

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Drug-like inhibitors of protein-protein interactions: a structural examination of effective protein mimicry

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Targeting protein-protein interactions for therapeutic intervention: a challenge for the future.

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

The inhibitor of apoptosis proteins as therapeutic targets in cancer

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Fragment-based design of small molecule X-linked inhibitor of apoptosis protein inhibitors

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2010.523697

The impact of GPCR structures on pharmacology and structure-based drug design

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Structure-based discovery of A2A adenosine receptor ligands

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Assessing synthetic accessibility of chemical compounds using machine learning methods

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Route Designer: a retrosynthetic analysis tool utilizing automated retrosynthetic rule generation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2010.523697

Free energy, entropy, and induced fit in host-guest recognition: calculations with the second-generation mining minima algorithm

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441.2010.523697

10.1517/17460441.2010.523697

21 January 2018

Identifiers

DOI

1 reference

27 August 2017

1 reference

PubMed ID

22827744