Automated site preparation in physics-based rescoring of receptor ligand complexes (Q37348271)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19382204%20AND%20SRC:MED&resulttype=core&format=json

26 January 2020

title

Automated site preparation in physics-based rescoring of receptor ligand complexes (English)

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26 January 2020

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26 January 2020

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19382204%20AND%20SRC:MED&resulttype=core&format=json

26 January 2020

Chaya S Rapp

1 reference

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26 January 2020

Cheryl Schonbrun

series ordinal

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26 January 2020

Chakrapani Kalyanaraman

series ordinal

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26 January 2020

language of work or name

English

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publication date

1 October 2009

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26 January 2020

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26 January 2020

volume

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26 January 2020

issue

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26 January 2020

page(s)

52-61

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Very fast prediction and rationalization of pKa values for protein-ligand complexes

26 January 2020

cites work

1 reference

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The Catalytic Mechanism of an Aspartic Proteinase Explored with Neutron and X-ray Diffraction

9 September 2017

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Rescoring Docking Hit Lists for Model Cavity Sites: Predictions and Experimental Testing

9 September 2017

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Discovery of kinase inhibitors by high-throughput docking and scoring based on a transferable linear interaction energy model

9 September 2017

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Caught in the Act: The 1.5 Å Resolution Crystal Structures of the HIV-1 Protease and the I54V Mutant Reveal a Tetrahedral Reaction Intermediate †

9 September 2017

1 reference

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Modeling of metal interaction geometries for protein-ligand docking.

9 September 2017

1 reference

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

9 September 2017

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A flexible approach to induced fit docking

9 September 2017

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Flexible ligand-flexible protein docking in protein kinase systems

9 September 2017

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Validation of an automated procedure for the prediction of relative free energies of binding on a set of aldose reductase inhibitors

9 September 2017

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Physics-based methods for studying protein-ligand interactions

9 September 2017

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Solvated interaction energy (SIE) for scoring protein-ligand binding affinities. 1. Exploring the parameter space.

9 September 2017

1 reference

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Molecular mechanics methods for predicting protein-ligand binding.

9 September 2017

1 reference

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Assignment of polar states for protein amino acid residues using an interaction cluster decomposition algorithm and its application to high resolution protein structure modeling.

9 September 2017

1 reference

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Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes

9 September 2017

1 reference

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A critical assessment of docking programs and scoring functions

9 September 2017

1 reference

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Parameter estimation for scoring protein-ligand interactions using negative training data

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

Prediction of protein-ligand interactions. Docking and scoring: successes and gaps

9 September 2017

1 reference

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Protein-ligand docking: current status and future challenges

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

On evaluating molecular-docking methods for pose prediction and enrichment factors

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

Comparison of consensus scoring strategies for evaluating computational models of protein-ligand complexes

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

Novel procedure for modeling ligand/receptor induced fit effects.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

A hierarchical approach to all-atom protein loop prediction

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

Ligand-protein database: linking protein-ligand complex structures to binding data

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

Thermodynamic dissection of the binding energetics of KNI-272, a potent HIV-1 protease inhibitor

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

9 September 2017

The Protein Data Bank

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Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation

9 September 2017

1 reference

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Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

WHAT IF: a molecular modeling and drug design program

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

A general approach for developing system-specific functions to score protein-ligand docked complexes using support vector inductive logic programming.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

Theoretical calculation of the binding free energies for pyruvate dehydrogenase E1 binding with ligands

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

Bias, reporting, and sharing: computational evaluations of docking methods

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

Redesigning protein pKa values.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

Electrostatics of ligand binding: parametrization of the generalized Born model and comparison with the Poisson-Boltzmann approach

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

Binding of phosphinate and phosphonate inhibitors to aspartic proteases: a first-principles study

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE).

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

Consensus scoring with feature selection for structure-based virtual screening

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

Maximum common binding modes (MCBM): consensus docking scoring using multiple ligand information and interaction fingerprints

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

A statistical rescoring scheme for protein-ligand docking: Consideration of entropic effect.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

High quality binding modes in docking ligands to proteins.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

Efficient comprehensive scoring of docked protein complexes using probabilistic support vector machines.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

FLIPDock: docking flexible ligands into flexible receptors.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

The consequences of scoring docked ligand conformations using free energy correlations.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

The use of consensus scoring in ligand-based virtual screening

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

Physics-based scoring of protein-ligand complexes: enrichment of known inhibitors in large-scale virtual screening

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

Assessing scoring functions for protein-ligand interactions

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

High-resolution prediction of protein helix positions and orientations

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

A fast estimate of electrostatic group contributions to the free energy of protein-inhibitor binding.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

Calculations of enzymatic reactions: calculations of pKa, proton transfer reactions, and general acid catalysis reactions in enzymes.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

Structure modeling, ligand binding, and binding affinity calculation (LR-MM-PBSA) of human heparanase for inhibition and drug design

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

Protein-protein binding is often associated with changes in protonation state

20 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744578

Linear-scaling molecular orbital calculations for the pKa values of ionizable residues in proteins

3 December 2018

1 reference

12 December 2020

pKa prediction using group philicity

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

An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function

1 reference

12 December 2020

Protonation changes upon ligand binding to trypsin and thrombin: structural interpretation based on pK(a) calculations and ITC experiments

1 reference

12 December 2020

Role of binding entropy in the refinement of protein-ligand docking predictions: analysis based on the use of 11 scoring functions

1 reference

12 December 2020

Accuracy of binding mode prediction with a cascadic stochastic tunneling method

1 reference

12 December 2020

Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors

1 reference

12 December 2020

Receptor-specific scoring functions derived from quantum chemical models improve affinity estimates for in-silico drug discovery

1 reference

12 December 2020

Epik: a software program for pK( a ) prediction and protonation state generation for drug-like molecules

1 reference

12 December 2020

Can we use docking and scoring for hit-to-lead optimization?

1 reference

12 December 2020

Distance dependent scoring function for describing protein-ligand intermolecular interactions

1 reference

12 December 2020

Combining docking, molecular dynamics and the linear interaction energy method to predict binding modes and affinities for non-nucleoside inhibitors to HIV-1 reverse transcriptase

1 reference

12 December 2020

Improving Docking Accuracy through Molecular Mechanics Generalized Born Optimization and Scoring

1 reference

12 December 2020

Multiscale Optimization of a Truncated Newton Minimization Algorithm and Application to Proteins and Protein-Ligand Complexes

1 reference

12 December 2020

Structural origins of pH and ionic strength effects on protein stability. Acid denaturation of sperm whale apomyoglobin

1 reference

12 December 2020

Identifiers

DOI

10.1002/PROT.22415

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19382204%20AND%20SRC:MED&resulttype=core&format=json

26 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19382204%20AND%20SRC:MED&resulttype=core&format=json

26 January 2020

PubMed publication ID

19382204

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19382204%20AND%20SRC:MED&resulttype=core&format=json