Comparative binding energy analysis for binding affinity and target selectivity prediction (Q43273730)

18 November 2017

Comparative binding energy analysis for binding affinity and target selectivity prediction (English)

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18 November 2017

4

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18 November 2017

Rebecca C Wade

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author name string

Stefan Henrich

series ordinal

1

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18 November 2017

Isabella Feierberg

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2

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18 November 2017

Ting Wang

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3

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18 November 2017

language of work or name

English

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publication date

1 January 2010

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18 November 2017

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18 November 2017

78

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18 November 2017

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18 November 2017

135-153

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Prediction of drug binding affinities by comparative binding energy analysis.

18 November 2017

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Calculation of protein-ligand binding affinities.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Scoring functions for protein-ligand docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Quantitative analysis of substrate specificity of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Comparative binding energy analysis of the substrate specificity of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Comparative binding energy analysis of HIV-1 protease inhibitors: incorporation of solvent effects and validation as a powerful tool in receptor-based drug design.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Comparative binding energy (COMBINE) analysis of human neutrophil elastase inhibition by pyridone-containing trifluoromethylketones.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Simulation of alternative binding modes in a structure-based QSAR study of HIV-1 protease inhibitors

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Comparative structural and energetic analysis of WW domain-peptide interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

How optimal are the binding energetics of barnase and barstar?

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Nuclear receptor-DNA binding specificity: A COMBINE and Free-Wilson QSAR analysis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Comparative binding energy (COMBINE) analysis of influenza neuraminidase-inhibitor complexes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Serine protease mechanism and specificity

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

On the size of the active site in proteases. I. Papain

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Rapid and general profiling of protease specificity by using combinatorial fluorogenic substrate libraries

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Structure and interaction modes of thrombin

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

The bovine basic pancreatic trypsin inhibitor (Kunitz inhibitor): a milestone protein

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Biochemistry and clinical role of trypsinogens and pancreatic secretory trypsin inhibitor

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Targeting thrombin – rational drug design from natural mechanisms

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Optimal subsite occupancy and design of a selective inhibitor of urokinase.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Identification of novel binding interactions in the development of potent, selective 2-naphthamidine inhibitors of urokinase. Synthesis, structural analysis, and SAR of N-phenyl amide 6-substitution

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Crystals of the urokinase type plasminogen activator variant beta(c)-uPAin complex with small molecule inhibitors open the way towards structure-based drug design

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

3D-QSAR CoMFA studies on trypsin-like serine protease inhibitors: a comparative selectivity analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Development and validation of a genetic algorithm for flexible docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Classification of protein sequences by homology modeling and quantitative analysis of electrostatic similarity.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

21 January 2018

The Protein Data Bank

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Development of computational and graphical tools for analysis of movement and flexibility in large molecules.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Amino acid substitution matrices from protein blocks

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

webPIPSA: a web server for the comparison of protein interaction properties

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

WHAT IF: a molecular modeling and drug design program

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

The Amber biomolecular simulation programs

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Automatic atom type and bond type perception in molecular mechanical calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Automatic generation of 3D-atomic coordinates for organic molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

A novel serine protease inhibition motif involving a multi-centered short hydrogen bonding network at the active site

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Structural basis for selectivity of a small molecule, S1-binding, submicromolar inhibitor of urokinase-type plasminogen activator

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Structural and functional analyses of benzamidine-based inhibitors in complex with trypsin: implications for the inhibition of factor Xa, tPA, and urokinase.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Factorising ligand affinity: a combined thermodynamic and crystallographic study of trypsin and thrombin inhibition

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Insight into the structural requirements of urokinase-type plasminogen activator inhibitors based on 3D QSAR CoMFA/CoMSIA models

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Engineering inhibitors highly selective for the S1 sites of Ser190 trypsin-like serine protease drug targets

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Electrostatic complementarity within the substrate-binding pocket of trypsin

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Residue Asp-189 controls both substrate binding and the monovalent cation specificity of thrombin

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Dissecting and designing inhibitor selectivity determinants at the S1 site using an artificial Ala190 protease (Ala190 uPA)

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Exploiting subsite S1 of trypsin-like serine proteases for selectivity: potent and selective inhibitors of urokinase-type plasminogen activator

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Structure-directed discovery of potent non-peptidic inhibitors of human urokinase that access a novel binding subsite.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Application of fragment screening and fragment linking to the discovery of novel thrombin inhibitors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Comparison of automated docking programs as virtual screening tools

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Lessons in molecular recognition: the effects of ligand and protein flexibility on molecular docking accuracy.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Design of novel and selective inhibitors of urokinase-type plasminogen activator with improved pharmacokinetic properties for use as antimetastatic agents

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

2-(2-Hydroxy-3-alkoxyphenyl)-1H-benzimidazole-5-carboxamidine derivatives as potent and selective urokinase-type plasminogen activator inhibitors

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

4-Aminoarylguanidine and 4-aminobenzamidine derivatives as potent and selective urokinase-type plasminogen activator inhibitors

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Comparative binding energy analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Comparative Binding Energy (COMBINE) Analysis of OppA−Peptide Complexes to Relate Structure to Binding Thermodynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22579

21 January 2018

Identifiers

DOI

10.1002/PROT.22579

1 reference

18 November 2017

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