Building a virtual ligand screening pipeline using free software: a survey (Q30044592)

20 June 2019

19 September 2019

12 August 2020

The Chemistry Development Kit (CDK): an open-source Java library for Chemo- and Bioinformatics

10 November 2020

0 references

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Bioclipse: an open source workbench for chemo- and bioinformatics

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

rDock: a fast, versatile and open source program for docking ligands to proteins and nucleic acids

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

KNIME-CDK: Workflow-driven cheminformatics

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

The Protein Model Portal--a comprehensive resource for protein structure and model information

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Open Babel: An open chemical toolbox

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

SwissDock, a protein-small molecule docking web service based on EADock DSS

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

DOCK 6: combining techniques to model RNA-small molecule complexes

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

The SWISS-MODEL Repository and associated resources

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Flexible ligand docking to multiple receptor conformations: a practical alternative

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

SuperTarget and Matador: resources for exploring drug-target relationships

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Relating protein pharmacology by ligand chemistry

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Benchmarking sets for molecular docking

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

26 May 2017

PMF scoring revisited

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

eHiTS: a new fast, exhaustive flexible ligand docking system

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

BALLView: an object-oriented molecular visualization and modeling framework

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

The Amber biomolecular simulation programs

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

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

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

UCSF Chimera--a visualization system for exploratory research and analysis

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Taverna: a tool for the composition and enactment of bioinformatics workflows

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

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

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Prediction of potential toxicity and side effect protein targets of a small molecule by a ligand-protein inverse docking approach

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

26 May 2017

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

VERIFY3D: assessment of protein models with three-dimensional profiles

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Development and validation of a genetic algorithm for flexible docking

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

VMD: visual molecular dynamics

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

WHAT IF: a molecular modeling and drug design program

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

YASARA View - molecular graphics for all devices - from smartphones to workstations

26 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Lead- and drug-like compounds: the rule-of-five revolution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Docking covalent inhibitors: a parameter free approach to pose prediction and scoring.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

A Bayesian statistical approach of improving knowledge-based scoring functions for protein-ligand interactions.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Drug2Gene: an exhaustive resource to explore effectively the drug-target relation network

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Making sense of large-scale kinase inhibitor bioactivity data sets: a comparative and integrative analysis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Boosting virtual screening enrichments with data fusion: coalescing hits from two-dimensional fingerprints, shape, and docking

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Structure-based design of conformationally flexible reverse transcriptase inhibitors to combat resistant HIV.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Structural basis of resistance to anti-cytochrome bc₁ complex inhibitors: implication for drug improvement

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Homology modeling a fast tool for drug discovery: current perspectives

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Drug discovery applications for KNIME: an open source data mining platform

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Conformational selection or induced fit? A critical appraisal of the kinetic mechanism

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

idTarget: a web server for identifying protein targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approach

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

The experimental uncertainty of heterogeneous public K(i) data.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

PDB_REDO: automated re-refinement of X-ray structure models in the PDB.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Going further than Lipinski's rule in drug design

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

ChemT, an open-source software for building template-based chemical libraries.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Multilevel Parallelization of AutoDock 4.2.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Self-organizing molecular fingerprints: a ligand-based view on drug-like chemical space and off-target prediction

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

iGEMDOCK: a graphical environment of enhancing GEMDOCK using pharmacological interactions and post-screening analysis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

FRED pose prediction and virtual screening accuracy

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Comprehensive comparison of ligand-based virtual screening tools against the DUD data set reveals limitations of current 3D methods.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Identification and validation of novel human pregnane X receptor activators among prescribed drugs via ligand-based virtual screening

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

GAPE: an improved genetic algorithm for pharmacophore elucidation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

VoteDock: consensus docking method for prediction of protein-ligand interactions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Predicting the accuracy of protein-ligand docking on homology models.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Induced fit, conformational selection and independent dynamic segments: an extended view of binding events

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Drug-like bioactive structures and conformational coverage with the LigPrep/ConfGen suite: comparison to programs MOE and catalyst

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Inclusion of solvation and entropy in the knowledge-based scoring function for protein-ligand interactions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

MultiCASE Expert Systems and the REACH Initiative

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Maximum unbiased validation (MUV) data sets for virtual screening based on PubChem bioactivity data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

SplitPocket: identification of protein functional surfaces and characterization of their spatial patterns

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Docking and scoring with alternative side-chain conformations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

SuperPred: drug classification and target prediction

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

PharmaGist: a webserver for ligand-based pharmacophore detection

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

MM-GB/SA rescoring of docking poses in structure-based lead optimization.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Binding MOAD, a high-quality protein-ligand database.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Identification of natural-product-derived inhibitors of 5-lipoxygenase activity by ligand-based virtual screening

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

eHiTS: an innovative approach to the docking and scoring function problems.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual ligand screening

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Recent advances in computational prediction of drug absorption and permeability in drug discovery

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

TarFisDock: a web server for identifying drug targets with docking approach

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

A limited universe of membrane protein families and folds

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Molecular descriptors and methods for ligand based virtual high throughput screening in drug discovery

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

MolDock: a new technique for high-accuracy molecular docking

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

SOMA--workflow for small molecule property calculations on a multiplatform computing grid

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Predicting protein druggability

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

KDE Bioscience: platform for bioinformatics analysis workflows.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Molecular mechanisms of drug resistance

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Update on NCI in vitro drug screen utilities

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Discovery of a novel binding trench in HIV integrase.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

MODBASE, a database of annotated comparative protein structure models, and associated resources.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

In silico prediction of drug toxicity

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Dynamic QSAR techniques: applications in drug design and toxicology

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

SLATE: a method for the superposition of flexible ligands.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

CombiDOCK: structure-based combinatorial docking and library design

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Prediction of rodent carcinogenicity using the DEREK system for 30 chemicals currently being tested by the National Toxicology Program. The DEREK Collaborative Group

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

COMPACT and molecular structure in toxicity assessment: a prospective evaluation of 30 chemicals currently being tested for rodent carcinogenicity by the NCI/NTP

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Automated docking of substrates to proteins by simulated annealing

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Structure-based strategies for drug design and discovery

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

What has virtual screening ever done for drug discovery?

3 June 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Performance of 3D-database molecular docking studies into homology models

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

PubChem: Integrated Platform of Small Molecules and Biological Activities

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

ChemSpider: An Online Chemical Information Resource

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

DoGSiteScorer: a web server for automatic binding site prediction, analysis and druggability assessment

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

PROCHECK: a program to check the stereochemical quality of protein structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

MetaPocket: a meta approach to improve protein ligand binding site prediction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Representing structural information with RasMol

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

AcquaAlta: a directional approach to the solvation of ligand-protein complexes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

An evaluation of automated homology modelling methods at low target template sequence similarity

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Influence of protonation, tautomeric, and stereoisomeric states on protein-ligand docking results

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Effect of atomic charge, solvation, entropy, and ligand protonation state on MM-PB(GB)SA binding energies of HIV protease.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

BetaDock: shape-priority docking method based on beta-complex.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

FLIPDock: docking flexible ligands into flexible receptors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Representing receptor flexibility in ligand docking through relevant normal modes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Docking ligands into flexible and solvated macromolecules. 1. Development and validation of FITTED 1.0.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Improving molecular docking through eHiTS' tunable scoring function.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

DOCKTITE-a highly versatile step-by-step workflow for covalent docking and virtual screening in the molecular operating environment.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

CovalentDock: automated covalent docking with parameterized covalent linkage energy estimation and molecular geometry constraints

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Combination of a naive Bayes classifier with consensus scoring improves enrichment of high-throughput docking results.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Supervised consensus scoring for docking and virtual screening.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Comparison of several molecular docking programs: pose prediction and virtual screening accuracy.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Modeling water molecules in protein-ligand docking using GOLD.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

A fast flexible docking method using an incremental construction algorithm.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Improved protein-ligand binding affinity prediction by using a curvature-dependent surface-area model

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

ID-Score: a new empirical scoring function based on a comprehensive set of descriptors related to protein-ligand interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Knowledge-based scoring function to predict protein-ligand interactions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

General and targeted statistical potentials for protein-ligand interactions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Application of a post-docking procedure based on MM-PBSA and MM-GBSA on single and multiple protein conformations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Comparison of structure- and ligand-based virtual screening protocols considering hit list complementarity and enrichment factors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Molecular docking using shape descriptors

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Task-parallel message passing interface implementation of Autodock4 for docking of very large databases of compounds using high-performance super-computers

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Accelerating molecular docking calculations using graphics processing units.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Kinase domain mutations in cancer: implications for small molecule drug design strategies.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Scoring ligand similarity in structure-based virtual screening.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Fast docking using the CHARMM force field with EADock DSS.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

GalaxyDock2: protein-ligand docking using beta-complex and global optimization

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

ICM?A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Molecular docking with ligand attached water molecules.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Feature trees: a new molecular similarity measure based on tree matching.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Open3DQSAR: a new open-source software aimed at high-throughput chemometric analysis of molecular interaction fields.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Similarity by compression.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

A fast new approach to pharmacophore mapping and its application to dopaminergic and benzodiazepine agonists.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

A genetic algorithm for flexible molecular overlay and pharmacophore elucidation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

GALAHAD: 1. pharmacophore identification by hypermolecular alignment of ligands in 3D.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

FLEXS: a method for fast flexible ligand superposition.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

A unified, probabilistic framework for structure- and ligand-based virtual screening.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Machine learning methods for property prediction in chemoinformatics: Quo Vadis?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

The Importance of Being Earnest: Validation is the Absolute Essential for Successful Application and Interpretation of QSPR Models

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Predicting drug metabolism--an evaluation of the expert system METEOR.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Assessment and validation of US EPA's OncoLogic® expert system and analysis of its modulating factors for structural alerts.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Effectiveness of CASE Ultra Expert System in Evaluating Adverse Effects of Drugs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Optimizing predictive performance of CASE Ultra expert system models using the applicability domains of individual toxicity alerts.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

ProTox: a web server for the in silico prediction of rodent oral toxicity

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Evaluation of the OECD (Q)SAR Application Toolbox and Toxtree for predicting and profiling the carcinogenic potential of chemicals

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

SwissTargetPrediction: a web server for target prediction of bioactive small molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

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/10.1093%2FBIB%2FBBV037

Scientific workflow management and the Kepler system

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV037

Feature selection for descriptor based classification models. 1. Theory and GA-SEC algorithm.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

META. 3. A genetic algorithm for metabolic transform priorities optimization.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793892

Zanamivir (Relenza )--a new treatment for influenza

26 November 2018

1 reference

12 December 2020

Performance of similarity measures in 2D fragment-based similarity searching: comparison of structural descriptors and similarity coefficients

1 reference

12 December 2020

Assessment of the oral rat chronic lowest observed adverse effect level model in TOPKAT, a QSAR software package for toxicity prediction

1 reference

12 December 2020

Identification of phosphodiesterase-1 and 5 dual inhibitors by a ligand-based virtual screening optimized for lead evolution

1 reference

12 December 2020

GlamDock: development and validation of a new docking tool on several thousand protein-ligand complexes

1 reference

12 December 2020

Ramachandran plot on the web (2.0)

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

ReverseScreen3D: a structure-based ligand matching method to identify protein targets

1 reference

12 December 2020

DSX: a knowledge-based scoring function for the assessment of protein-ligand complexes

1 reference

12 December 2020

IUPAC-IUB Commission on Biochemical Nomenclature. Abbreviations and symbols for the description of the conformation of polypeptide chains

1 reference

12 December 2020

MS-WHIM, new 3D theoretical descriptors derived from molecular surface properties: a comparative 3D QSAR study in a series of steroids

1 reference

12 December 2020

Screening a peptidyl database for potential ligands to proteins with side-chain flexibility

1 reference

12 December 2020

Identifiers

0 references

1 reference

DBLP Dataset 2021-01-02

release_jwhqn6n3hnh4pjtcmbgv4jq6ia

28 January 2021

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/jwhqn6n3hnh4pjtcmbgv4jq6ia

24 November 2022