A consistent description of HYdrogen bond and DEhydration energies in protein-ligand complexes: methods behind the HYDE scoring function (Q28282247)

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

Comparative assessment of scoring functions on a diverse test set.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

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/10.1007%2FS10822-012-9626-2

The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

A fast flexible docking method using an incremental construction algorithm.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

A medicinal chemist's guide to molecular interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

SFCscore: scoring functions for affinity prediction of protein-ligand complexes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

Rapid context-dependent ligand desolvation in molecular docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

Very empirical treatment of solvation and entropy: a force field derived from log Po/w

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

Further development and validation of empirical scoring functions for structure-based binding affinity prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

Substantial improvements in large-scale redocking and screening using the novel HYDE scoring function

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

Areas, volumes, packing and protein structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

Solvent-accessible surfaces of proteins and nucleic acids

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

Analytical molecular surface calculation

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

A force field with discrete displaceable waters and desolvation entropy for hydrated ligand docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

Nearly no Scoring Function Without a Hansch-Analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

The interpretation of protein structures: Estimation of static accessibility

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

Environment and exposure to solvent of protein atoms. Lysozyme and insulin

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

van der Waals Volumes and Radii

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

Modeling of metal interaction geometries for protein-ligand docking.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

Fast automated placement of polar hydrogen atoms in protein-ligand complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

The PDBbind database: methodologies and updates

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

Development and validation of a genetic algorithm for flexible docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

Improved protein-ligand docking using GOLD

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

Empirical scoring functions for advanced protein-ligand docking with PLANTS.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

Benchmarking sets for molecular docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

More than a simple lipophilic contact: a detailed thermodynamic analysis of nonbasic residues in the s1 pocket of thrombin.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

21 January 2018

The Protein Data Bank

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

PHOENIX: a scoring function for affinity prediction derived using high-resolution crystal structures and calorimetry measurements

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

Comparison of Automatic Three-Dimensional Model Builders Using 639 X-ray Structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

ZINC--a free database of commercially available compounds for virtual screening

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

Docking performance of the glide program as evaluated on the Astex and DUD datasets: a complete set of glide SP results and selected results for a new scoring function integrating WaterMap and glide

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

Pose prediction and virtual screening performance of GOLD scoring functions in a standardized test.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

Docking and scoring with ICM: the benchmarking results and strategies for improvement

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

FRED pose prediction and virtual screening accuracy

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

Evaluation of DOCK 6 as a pose generation and database enrichment tool

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

Towards an Integrated Description of Hydrogen Bonding and Dehydration: Decreasing False Positives in Virtual Screening with the HYDE Scoring Function

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9626-2

Structural artifacts in protein-ligand X-ray structures: implications for the development of docking scoring functions

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23269578

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

LigScore: a novel scoring function for predicting binding affinities

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23269578