3D-RISM-Dock: A New Fragment-Based Drug Design Protocol (Q40276857)

19 September 2017

title

3D-RISM-Dock: A New Fragment-Based Drug Design Protocol (English)

1 reference

19 September 2017

3

1 reference

19 September 2017

Dragan Nikolić

1

1 reference

19 September 2017

Nikolay Blinov

series ordinal

2

1 reference

19 September 2017

Andriy Kovalenko

series ordinal

4

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19 September 2017

publication date

21 August 2012

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Journal of Chemical Theory and Computation

19 September 2017

published in

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19 September 2017

volume

8

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19 September 2017

issue

9

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19 September 2017

page(s)

3356-3372

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Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock

19 September 2017

cites work

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Calculation of local water densities in biological systems: a comparison of molecular dynamics simulations and the 3D-RISM-KH molecular theory of solvation

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Automated docking and the search for HIV protease inhibitors

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5 May 2024

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An MM/3D-RISM approach for ligand binding affinities.

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The MoD-QM/MM methodology for structural refinement of photosystem II and other biological macromolecules.

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Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements

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Multiple-site titration and molecular modeling: two rapid methods for computing energies and forces for ionizable groups in proteins

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Iterative partial equalization of orbital electronegativity—a rapid access to atomic charges

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AutoGrow: a novel algorithm for protein inhibitor design

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5 May 2024

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Electrostatics of nanosystems: application to microtubules and the ribosome

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5 May 2024

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Flexible ligand docking using evolutionary algorithms: investigating the effects of variation operators and local search hybrids.

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5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Optimization of parameters for semiempirical methods IV: extension of MNDO, AM1, and PM3 to more main group elements

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5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Topological analysis of the electron density in model azolium systems for thiamin structure-function: sulfur is the electron sink and positively polarized carbanions act as nucleophiles

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5 May 2024

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

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5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures

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5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

PMF scoring revisited

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5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Structure-function relationships in pyruvate decarboxylase of yeast and wheat germ

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5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

DynaDock: A new molecular dynamics-based algorithm for protein-peptide docking including receptor flexibility.

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5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Structural insights into the interaction between prion protein and nucleic acid

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5 May 2024

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A simple clustering algorithm can be accurate enough for use in calculations of pKs in macromolecules

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5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Insights into Mycoplasma genitalium metabolism revealed by the structure of MG289, an extracytoplasmic thiamine binding lipoprotein

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Solid-state NMR and density functional theory studies of ionization states of thiamin.

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

DOVIS 2.0: an efficient and easy to use parallel virtual screening tool based on AutoDock 4.0.

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5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Molecular docking and ligand specificity in fragment-based inhibitor discovery

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5 May 2024

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A new Lamarckian genetic algorithm for flexible ligand-receptor docking

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5 May 2024

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

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Modified AutoDock for accurate docking of protein kinase inhibitors

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Strike a balance: optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

RM1: a reparameterization of AM1 for H, C, N, O, P, S, F, Cl, Br, and I

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Efficient docking of peptides to proteins without prior knowledge of the binding site

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

The missing term in effective pair potentials

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Parallel implementation ofAutoDock

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Application of the PM6 method to modeling proteins

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Massive docking of flexible ligands using environmental niches in parallelized genetic algorithms

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Dockres: a computer program that analyzes the output of virtual screening of small molecules

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

H++: a server for estimating pKas and adding missing hydrogens to macromolecules

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Critical assessment of the automated AutoDock as a new docking tool for virtual screening.

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Assessing scoring functions for protein-ligand interactions

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

VSDocker: a tool for parallel high-throughput virtual screening using AutoDock on Windows-based computer clusters.

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

A common structural motif in thiamin pyrophosphate-binding enzymes

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5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Virtual screening: an endless staircase?

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5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

A New Approach for Investigating the Molecular Recognition of Protein: Toward Structure-Based Drug Design Based on the 3D-RISM Theory.

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Optimization of parameters for semiempirical methods. III Extension of PM3 to Be, Mg, Zn, Ga, Ge, As, Se, Cd, In, Sn, Sb, Te, Hg, Tl, Pb, and Bi

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Automated docking of flexible ligands: applications of AutoDock

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Virtual screening of chemical libraries

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

DOVIS: an implementation for high-throughput virtual screening using AutoDock

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Comparison of ligand- and structure-based virtual screening on the DUD data set.

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Development and testing of a general amber force field

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Locating missing water molecules in protein cavities by the three-dimensional reference interaction site model theory of molecular solvation.

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

A semiempirical free energy force field with charge-based desolvation

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Ligand mapping on protein surfaces by the 3D-RISM theory: toward computational fragment-based drug design

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Predicting absolute ligand binding free energies to a simple model site

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

A new force field for molecular mechanical simulation of nucleic acids and proteins

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Force fields for protein simulations

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Self-consistent description of a metal–water interface by the Kohn–Sham density functional theory and the three-dimensional reference interaction site model

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent.

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

The effect of different electrostatic potentials on docking accuracy: A case study using DOCK5.4

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Is a hydrophobic amino acid required to maintain the reactive V conformation of thiamin at the active center of thiamin diphosphate-requiring enzymes? Experimental and computational studies of isoleucine 415 of yeast pyruvate decarboxylase

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5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Non-charged thiamine analogs as inhibitors of enzyme transketolase.

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5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Analytical electrostatics for biomolecules: beyond the generalized Born approximation

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Semiempirical calculations on the electronic structure and preferred conformation of thiamine (vitamin B1) and thiamine pyrophosphate (cocarboxylase)

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Valence, Oxidation Number, and Formal Charge: Three Related but Fundamentally Different Concepts

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5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

Role of bridging water molecules in GSK3β-inhibitor complexes: insights from QM/MM, MD, and molecular docking studies.

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

An analysis of 3D solvation structure in biomolecules: application to coiled coil serine and bacteriorhodopsin

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5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

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5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

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

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5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

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5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions

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5 May 2024

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Distinguish protein decoys by using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model

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5 May 2024

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Ground states of molecules. 38. The MNDO method. Approximations and parameters

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5 May 2024

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Hydrophobic cooperativity as a mechanism for amyloid nucleation

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5 May 2024

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Construction of a thiamin sensor from the periplasmic thiamin binding protein

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5 May 2024

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Solution structure of a 142-residue recombinant prion protein corresponding to the infectious fragment of the scrapie isoform

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5 May 2024

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Virtual screening strategies in drug discovery

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5 May 2024

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Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values.

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5 May 2024

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Protein-ligand docking: current status and future challenges

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5 May 2024

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Coenzyme Binding in Yeast Pyruvate Decarboxylase. A Fluorescent Enzyme-Inhibitor Complex

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5 May 2024

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Hot spots in prion protein for pathogenic conversion

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5 May 2024

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Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation

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5 May 2024

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Virtual Screening with AutoDock: Theory and Practice

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5 May 2024

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In silico antitarget screening

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5 May 2024

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Additivity principles in biochemistry

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5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

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

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1021/CT300257V

HMDB: a knowledgebase for the human metabolome

2 references

5 May 2024

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5 May 2024

https://opencitations.net/index/api/v1/citations/10.1093/NAR/GKN810

Mechanism of the hydrophobic effect in the biomolecular recognition of arylsulfonamides by carbonic anhydrase

1 reference

5 May 2024

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Identifiers

DOI

10.1021/CT300257V

1 reference

19 September 2017

1 reference