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Title: Molecular Dynamics Simulations of the Antithrombin upon Ligand Recognition: A MM/GBSA Approach

Conference ·
; ;

Research Organization:
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Sponsoring Organization:
USDOE
DOE Contract Number:
DE-AC52-07NA27344
OSTI ID:
1182228
Report Number(s):
LLNL-CONF-665482
Resource Relation:
Journal Volume: 9044; Conference: Presented at: 2015 International Work-Conference on Bioinformatics and Biomedical Engineering, Granada , Spain, Apr 15 - Apr 17, 2015
Country of Publication:
United States
Language:
English

References (23)

Toward Fully Automated High Performance Computing Drug Discovery: A Massively Parallel Virtual Screening Pipeline for Docking and Molecular Mechanics/Generalized Born Surface Area Rescoring to Improve Enrichment journal December 2013
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Calculating Structures and Free Energies of Complex Molecules:  Combining Molecular Mechanics and Continuum Models journal December 2000
Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations journal November 2010
Improving drug discovery using hybrid softcomputing methods journal July 2014
High-Throughput parallel blind Virtual Screening using BINDSURF journal January 2012
MM/GBSA Binding Energy Prediction on the PDBbind Data Set: Successes, Failures, and Directions for Further Improvement
  • Greenidge, Paulette A.; Kramer, Christian; Mozziconacci, Jean-Christophe
  • Journal of Chemical Information and Modeling, Vol. 53, Issue 1 https://doi.org/10.1021/ci300425v
journal December 2012
Compensating Enthalpic and Entropic Changes Hinder Binding Affinity Optimization journal June 2007
Carbohydrate isoforms of antithrombin variant N135Q with different heparin affinities journal November 1993
The anticoagulant activation of antithrombin by heparin journal December 1997
Further characterization of the antithrombin-binding sequence in heparin journal January 1982
Insights into the induced fit mechanism in antithrombin–heparin interaction using molecular dynamics simulations journal December 2005
Effects of glycosylation on heparin binding and antithrombin activation by heparin: Asn135 Glycan Roles on Antithrombin Activity
  • Pol-Fachin, Laercio; Franco Becker, Camila; Almeida Guimarães, Jorge
  • Proteins: Structure, Function, and Bioinformatics, Vol. 79, Issue 9 https://doi.org/10.1002/prot.23102
journal July 2011
Docking of Glycosaminoglycans to Heparin-Binding Proteins:  Validation for aFGF, bFGF, and Antithrombin and Application to IL-8 journal April 1999
Comparison of stochastic optimization methods for receptor–ligand docking journal August 2002
In Silico Discovery of a Compound with Nanomolar Affinity to Antithrombin Causing Partial Activation and Increased Heparin Affinity journal July 2012
Development and testing of a general amber force field journal January 2004
Automatic atom type and bond type perception in molecular mechanical calculations journal October 2006
Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method journal January 2000
The Amber biomolecular simulation programs journal January 2005
Exploring protein native states and large-scale conformational changes with a modified generalized born model journal March 2004
Ligand Binding Efficiency: Trends, Physical Basis, and Implications journal April 2008

Similar Records

Molecular Dynamics Simulations of the Antithrombin upon Ligand Recognition: A MM/GBSA Approach
Journal Article · Thu Jan 15 00:00:00 EST 2015 · Bioinformatics and Biomedical Engineering, Lecture Notes in Computer Science, na, na, April 15, 2015, pp. 584-593 · OSTI ID:1182228
A Comprehensive Docking and MM/GBSA Rescoring Study of Ligand Recognition upon Binding Antithrombin
Journal Article · Thu Apr 06 00:00:00 EDT 2017 · Current Topics in Medicinal Chemistry · OSTI ID:1182228
Towards fully automated high performance computing drug discovery: A massively parallel virtual screening pipeline for docking and MM/GBSA rescoring to improve enrichment
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Related Subjects

59 BASIC BIOLOGICAL SCIENCES