BetaDock: shape-priority docking method based on beta-complex. (Q51555332)

7 April 2018

title

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

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7 April 2018

8

Jong Bhak

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7 April 2018

author name string

Deok-Soo Kim

1

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7 April 2018

Chong-Min Kim

2

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7 April 2018

Chung-In Won

3

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7 April 2018

Jae-Kwan Kim

4

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7 April 2018

Joonghyun Ryu

5

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7 April 2018

Youngsong Cho

6

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7 April 2018

Changhee Lee

7

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7 April 2018

publication date

1 August 2011

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7 April 2018

Journal of Biomolecular Structure and Dynamics

published in

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7 April 2018

volume

29

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7 April 2018

issue

1

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7 April 2018

page(s)

219-242

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7 April 2018

Docking simulation and competitive experiments validate the interaction between the 2,5-xylidine inhibitor and Rigidoporus lignosus laccase

cites work

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Molecular modeling of Mycobacterium tuberculosis DNA gyrase and its molecular docking study with gatifloxacin inhibitors

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Virtual screening and drug design for PDE-5 receptor from traditional Chinese medicine database

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Structure-based and ligand-based drug design for HER 2 receptor

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Insight derived from molecular dynamics simulation into substrate-induced changes in protein motions of proteinase K.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

A novel strategy for designing the selective PPAR agonist by the "sum of activity" model

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Molecular docking studies to map the binding site of squalene synthase inhibitors on dehydrosqualene synthase of Staphylococcus aureus.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

A theoretical elucidation of glucose interaction with HSA's domains.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

A conformationally constrained peptidomimetic binds to the extracellular region of HER2 protein

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Anti-infectious bronchitis virus (IBV) activity of 1,8-cineole: effect on nucleocapsid (N) protein

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Key features for designing phosphodiesterase-5 inhibitors

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Weighted equation and rules--a novel concept for evaluating protein-ligand interaction

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

An insight to the dynamics of conserved water molecular triad in IMPDH II (human): recognition of cofactor and substrate to catalytic Arg 322.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Ligand-based dual target drug design for H1N1: swine flu--a preliminary first study

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Computational model of the HIV-1 subtype A V3 loop: study on the conformational mobility for structure-based anti-AIDS drug design

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Construction and assessment of reaction models of class I EPSP synthase: molecular docking and density functional theoretical calculations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

A docking study using atomistic conformers generated via elastic network model for cyclosporin A/cyclophilin A complex.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Computer-aided drug design of novel PLA2 inhibitor candidates for treatment of snakebite

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Computational studies of human galectin-1: role of conserved tryptophan residue in stacking interaction with carbohydrate ligands.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Molecular modeling of human pentameric alpha(7) neuronal nicotinic acetylcholine receptor and its interaction with its agonist and competitive antagonist

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Homology modeling of GLUT4, an insulin regulated facilitated glucose transporter and docking studies with ATP and its inhibitors

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Empirical force fields for biological macromolecules: overview and issues.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Molecular docking using shape descriptors

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

A combinatorial algorithm for calculating ligand binding

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Assessment of blind predictions of protein-protein interactions: current status of docking methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Prediction of protein-protein interactions by docking methods.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Design of new chemotherapeutics against the deadly anthrax disease. Docking and molecular dynamics studies of inhibitors containing pyrrolidine and riboamidrazone rings on nucleoside hydrolase from Bacillus anthracis

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Structural characterization of vivapain-2 and vivapain-3, cysteine proteases from Plasmodium vivax: comparative protein modeling and docking studies

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Homology modeling of wild-type, D516V, and H526L Mycobacterium tuberculosis RNA polymerase and their molecular docking study with inhibitors

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Molecular docking of the scorpion toxin Tc1 to the structural model of the voltage-gated potassium channel Kv1.1 from human Homo sapiens.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Ab initio protein structure prediction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Ab initio protein folding.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Ab initio construction of protein tertiary structures using a hierarchical approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

A semiempirical free energy force field with charge-based desolvation

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Substrate and docking interactions in serine/threonine protein kinases

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

The packing of α-helices: simple coiled-coils

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Application of a Theory of Enzyme Specificity to Protein Synthesis

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Analytical approximation to the accessible surface area of proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

A geometric approach to macromolecule-ligand interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Protein docking and complementarity

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Orientational sampling and rigid-body minimization in molecular docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Development and validation of a modular, extensible docking program: DOCK 5.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Protein-protein recognition analyzed by docking simulation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

PUZZLE: a new method for automated protein docking based on surface shape complementarity.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

"Soft docking": matching of molecular surface cubes

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Computational methods for biomolecular docking.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Hydrogen bonding and molecular surface shape complementarity as a basis for protein docking.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Molecular surface recognition by a computer vision-based technique

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Molecular surface complementarity at protein-protein interfaces: the critical role played by surface normals at well placed, sparse, points in docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Shape complementarity at protein-protein interfaces

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

21 January 2018

The Monte Carlo method

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Automated docking of substrates to proteins by simulated annealing

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Automated docking of flexible ligands: applications of AutoDock

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Minimization of polypeptide energy. I. Preliminary structures of bovine pancreatic ribonuclease S-peptide

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Study of protein-protein interaction using conformational space annealing.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Monte Carlo-minimization approach to the multiple-minima problem in protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Prediction of protein conformation on the basis of a search for compact structures: test on avian pancreatic polypeptide

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Development and validation of a genetic algorithm for flexible docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

EADock: docking of small molecules into protein active sites with a multiobjective evolutionary optimization.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

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/10.1080%2F07391102.2011.10507384

PSI-DOCK: towards highly efficient and accurate flexible ligand docking.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Molecular dynamics: survey of methods for simulating the activity of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Global optimization of clusters, crystals, and biomolecules.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Funnels, pathways, and the energy landscape of protein folding: a synthesis

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Protein folding funnels: a kinetic approach to the sequence-structure relationship

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Cavity search: an algorithm for the isolation and display of cavity-like binding regions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

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/10.1080%2F07391102.2011.10507384

A very fast program for visualizing protein surfaces, channels and cavities.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Fast prediction and visualization of protein binding pockets with PASS.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

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/10.1080%2F07391102.2011.10507384

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

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/10.1080%2F07391102.2011.10507384

A comparison of heuristic search algorithms for molecular docking.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Flexible docking using Tabu search and an empirical estimate of binding affinity.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Docking and scoring in virtual screening for drug discovery: methods and applications

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

A solution for the best rotation to relate two sets of vectors

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

The Hungarian method for the assignment problem

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Theoretical Improvements in Algorithmic Efficiency for Network Flow Problems

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Protein-ligand docking: current status and future challenges

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

On evaluating molecular-docking methods for pose prediction and enrichment factors

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

Estimating 3-D rigid body transformations: a comparison of four major algorithms

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2011.10507384

10.1080/07391102.2011.10507384

21 January 2018

Identifiers

DOI

1 reference

7 April 2018

PubMed ID

21696235

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7 April 2018