Computational Methods to Support Fragment-based Drug Discovery (Q58488998)

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Limitations and lessons in the use of X-ray structural information in drug design

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Protein-ligand cocrystal structures: we can do better

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Structure-based drug discovery and protein targets in the CNS.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Predicting druggable binding sites at the protein-protein interface.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

A hot spot of binding energy in a hormone-receptor interface

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Detection, delineation, measurement and display of cavities in macromolecular structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

A geometric approach to macromolecule-ligand interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

PocketPicker: analysis of ligand binding-sites with shape descriptors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Detection of multiscale pockets on protein surfaces using mathematical morphology.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

A novel and efficient tool for locating and characterizing protein cavities and binding sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Analyzing the topology of active sites: on the prediction of pockets and subpockets

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Roll: a new algorithm for the detection of protein pockets and cavities with a rolling probe sphere.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

On the nature of cavities on protein surfaces: application to the identification of drug-binding sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Fast prediction and visualization of protein binding pockets with PASS.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Fpocket: an open source platform for ligand pocket detection.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

A computational procedure for determining energetically favorable binding sites on biologically important macromolecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Highly accurate method for ligand-binding site prediction in unbound state (apo) protein structures.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Pocketome via comprehensive identification and classification of ligand binding envelopes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

SITEHOUND-web: a server for ligand binding site identification in protein structures.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Multiple solvent crystal structures: probing binding sites, plasticity and hydration

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

FTSite: high accuracy detection of ligand binding sites on unbound protein structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Multistructural hot spot characterization with FTProd

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Identification of potential small molecule binding pockets on Rho family GTPases

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Mapping of allosteric druggable sites in activation-associated conformers of the M2 muscarinic receptor

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Binding site detection and druggability index from first principles.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Full protein flexibility is essential for proper hot-spot mapping.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Computational fragment-based binding site identification by ligand competitive saturation

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Searching for likeness in a database of macromolecular complexes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Prediction of ligand binding sites using homologous structures and conservation at CASP8.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

A method for localizing ligand binding pockets in protein structures.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Identifying and characterizing binding sites and assessing druggability

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Structure-based druggability assessment--identifying suitable targets for small molecule therapeutics

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Large-scale prediction of drug-target relationships

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Structure-based computational analysis of protein binding sites for function and druggability prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Drug-like density: a method of quantifying the "bindability" of a protein target based on a very large set of pockets and drug-like ligands from the Protein Data Bank

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

DrugPred: a structure-based approach to predict protein druggability developed using an extensive nonredundant data set.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Development of a rule-based method for the assessment of protein druggability

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Combining global and local measures for structure-based druggability predictions

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Discovering novel ligands for macromolecules using X-ray crystallographic screening

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

The properties of known drugs. 1. Molecular frameworks

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

The SHAPES strategy: an NMR-based approach for lead generation in drug discovery.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Design and characterization of libraries of molecular fragments for use in NMR screening against protein targets.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Lessons for fragment library design: analysis of output from multiple screening campaigns

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Automatic and efficient decomposition of two-dimensional structures of small molecules for fragment-based high-throughput docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Identification and selection of "privileged fragments" suitable for primary screening

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Natural-product-derived fragments for fragment-based ligand discovery

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Discovery of Leukotriene A4 Hydrolase Inhibitors Using Metabolomics Biased Fragment Crystallography †

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Design of compound libraries for fragment screening

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Design of a fragment library that maximally represents available chemical space

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Enumeration of 166 billion organic small molecules in the chemical universe database GDB-17.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Visualization and virtual screening of the chemical universe database GDB-17.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Molecular docking and ligand specificity in fragment-based inhibitor discovery

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Docking for fragment inhibitors of AmpC -lactamase

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Docking performance of fragments and druglike compounds.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Grand canonical Monte Carlo simulation of ligand-protein binding.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Computational approaches for fragment-based and de novo design

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Chemical fragments that hydrogen bond to Asp, Glu, Arg, and His side chains in protein binding sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Residue preference mapping of ligand fragments in the Protein Data Bank

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

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/10.1002%2F9783527683604.CH09

A new target for shigellosis: rational design and crystallographic studies of inhibitors of tRNA-guanine transglycosylase

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Optimizing fragment and scaffold docking by use of molecular interaction fingerprints

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Benchmarking sets for molecular docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

QM/MM as a tool in fragment based drug discovery. A cross-docking, rescoring study of kinase inhibitors

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Energetic analysis of fragment docking and application to structure-based pharmacophore hypothesis generation

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Virtual fragment screening: an exploration of various docking and scoring protocols for fragments using Glide

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Fragment-Based flexible ligand docking by evolutionary optimization.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Hot spot analysis for driving the development of hits into leads in fragment-based drug discovery

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Fragment-based drug design: how big is too big?

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

The consequences of translational and rotational entropy lost by small molecules on binding to proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

In silico fragment-based drug discovery: setup and validation of a fragment-to-lead computational protocol using S4MPLE.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

CONFIRM: connecting fragments found in receptor molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

CAVEAT: a program to facilitate the design of organic molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

LEA3D: a computer-aided ligand design for structure-based drug design.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

FlexNovo: structure-based searching in large fragment spaces.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

BREED: Generating novel inhibitors through hybridization of known ligands. Application to CDK2, p38, and HIV protease.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Fragment-based de novo ligand design by multiobjective evolutionary optimization

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

De novo design of enzyme inhibitors by Monte Carlo ligand generation

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

An automated method for dynamic ligand design.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

SkelGen: a general tool for structure-based de novo ligand design.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Recent developments in fragment-based drug discovery

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09

Binding Response: A Descriptor for Selecting Ligand Binding Site on Protein Surfaces

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9783527683604.CH09