Protoss: a holistic approach to predict tautomers and protonation states in protein-ligand complexes (Q39556598)

13 September 2017

Protoss: a holistic approach to predict tautomers and protonation states in protein-ligand complexes (English)

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13 September 2017

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Matthias Rarey

4

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author name string

Stefan Bietz

series ordinal

1

1 reference

13 September 2017

Sascha Urbaczek

series ordinal

2

1 reference

13 September 2017

Benjamin Schulz

series ordinal

3

1 reference

13 September 2017

3 April 2014

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Journal of Cheminformatics

13 September 2017

1 reference

13 September 2017

6

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13 September 2017

12

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Creative Commons Attribution 2.0 Generic

13 September 2017

start time

3 April 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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April 2022 Public Data File from Crossref

cites work

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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.

14 September 2017

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sc-PDB: an annotated database of druggable binding sites from the Protein Data Bank

14 September 2017

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An assessment of the accuracy of methods for predicting hydrogen positions in protein structures.

14 September 2017

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14 September 2017

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Ligand Depot: a data warehouse for ligands bound to macromolecules

14 September 2017

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A graph-theory algorithm for rapid protein side-chain prediction

14 September 2017

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A fluorine scan of thrombin inhibitors to map the fluorophilicity/fluorophobicity of an enzyme active site: evidence for C-F...C=O interactions

14 September 2017

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Dynamic roles of arginine residues 82 and 92 of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: crystallographic studies

14 September 2017

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Discovery of a novel series of 6-azauracil-based thyroid hormone receptor ligands: potent, TR beta subtype-selective thyromimetics

14 September 2017

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Increasing the precision of comparative models with YASARA NOVA-a self-parameterizing force field

14 September 2017

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14 September 2017

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

14 September 2017

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

14 September 2017

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A method for determining the positions of polar hydrogens added to a protein structure that maximizes protein hydrogen bonding

14 September 2017

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Web application for studying the free energy of binding and protonation states of protein-ligand complexes based on HINT.

14 September 2017

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The valence state combination model: a generic framework for handling tautomers and protonation states

17 June 2018

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Reading PDB: perception of molecules from 3D atomic coordinates

21 August 2018

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Assignment of protonation states in proteins and ligands: combining pKa prediction with hydrogen bonding network optimization

21 August 2018

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NAOMI: on the almost trivial task of reading molecules from different file formats

21 August 2018

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Protonate3D: assignment of ionization states and hydrogen coordinates to macromolecular structures

21 August 2018

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Diverse, high-quality test set for the validation of protein-ligand docking performance.

21 August 2018

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Structure-based design of novel Chk1 inhibitors: insights into hydrogen bonding and protein-ligand affinity

21 August 2018

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Structure-based design, synthesis, and structure-activity relationship studies of novel non-nucleoside adenosine deaminase inhibitors

21 August 2018

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Structural basis for the autoinhibition and STI-571 inhibition of c-Kit tyrosine kinase

21 August 2018

1 reference

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A fast flexible docking method using an incremental construction algorithm.

21 August 2018

1 reference

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SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules

21 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186/1758-2946-6-12

SMILES. 2. Algorithm for generation of unique SMILES notation

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186/1758-2946-6-12

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

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186/1758-2946-6-12

21 January 2018

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1186/1758-2946-6-12

2 January 2022

Identifiers

DOI

10.1186/1758-2946-6-12

1 reference

journals/jcheminf/BietzUSR14

13 September 2017

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

1 reference

9 September 2019

https://scigraph.springernature.com/pub.10.1186/1758-2946-6-12

1 reference

13 September 2017

PubMed publication ID

24694216

1 reference