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Title: Customizable de novo design strategies for DOCK: Application to HIVgp41 and other therapeutic targets

Authors:
 [1];  [2];  [3]; ORCiD logo [4]
  1. Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook New York 11794
  2. Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook New York 11794
  3. Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco California 94158
  4. Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook New York 11794, Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook New York 11794, Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook New York 11794
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1393999
Grant/Contract Number:  
AC02-98CH10886
Resource Type:
Publisher's Accepted Manuscript
Journal Name:
Journal of Computational Chemistry
Additional Journal Information:
Journal Name: Journal of Computational Chemistry Journal Volume: 38 Journal Issue: 30; Journal ID: ISSN 0192-8651
Publisher:
Wiley Blackwell (John Wiley & Sons)
Country of Publication:
United States
Language:
English

Citation Formats

Allen, William J., Fochtman, Brian C., Balius, Trent E., and Rizzo, Robert C. Customizable de novo design strategies for DOCK: Application to HIVgp41 and other therapeutic targets. United States: N. p., 2017. Web. doi:10.1002/jcc.25052.
Allen, William J., Fochtman, Brian C., Balius, Trent E., & Rizzo, Robert C. Customizable de novo design strategies for DOCK: Application to HIVgp41 and other therapeutic targets. United States. doi:10.1002/jcc.25052.
Allen, William J., Fochtman, Brian C., Balius, Trent E., and Rizzo, Robert C. Fri . "Customizable de novo design strategies for DOCK: Application to HIVgp41 and other therapeutic targets". United States. doi:10.1002/jcc.25052.
@article{osti_1393999,
title = {Customizable de novo design strategies for DOCK: Application to HIVgp41 and other therapeutic targets},
author = {Allen, William J. and Fochtman, Brian C. and Balius, Trent E. and Rizzo, Robert C.},
abstractNote = {},
doi = {10.1002/jcc.25052},
journal = {Journal of Computational Chemistry},
number = 30,
volume = 38,
place = {United States},
year = {2017},
month = {9}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1002/jcc.25052

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Cited by: 2 works
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Works referenced in this record:

Implementation and evaluation of a docking-rescoring method using molecular footprint comparisons
journal, May 2011

  • Balius, Trent E.; Mukherjee, Sudipto; Rizzo, Robert C.
  • Journal of Computational Chemistry, Vol. 32, Issue 10
  • DOI: 10.1002/jcc.21814

Docking Screens for Novel Ligands Conferring New Biology: Miniperspective
journal, March 2016


From Docking False-Positive to Active Anti-HIV Agent
journal, November 2007

  • Barreiro, Gabriela; Kim, Joseph T.; Guimarães, Cristiano R. W.
  • Journal of Medicinal Chemistry, Vol. 50, Issue 22
  • DOI: 10.1021/jm070683u

Multi-Objective Molecular De Novo Design by Adaptive Fragment Prioritization
journal, March 2014

  • Reutlinger, Michael; Rodrigues, Tiago; Schneider, Petra
  • Angewandte Chemie International Edition, Vol. 53, Issue 16
  • DOI: 10.1002/anie.201310864

Phantom PAINS: Problems with the Utility of Alerts for P an- A ssay IN terference Compound S
journal, February 2017

  • Capuzzi, Stephen J.; Muratov, Eugene N.; Tropsha, Alexander
  • Journal of Chemical Information and Modeling, Vol. 57, Issue 3
  • DOI: 10.1021/acs.jcim.6b00465

Molecular Similarity Searching Using Atom Environments, Information-Based Feature Selection, and a Naïve Bayesian Classifier
journal, January 2004

  • Bender, Andreas; Mussa, Hamse Y.; Glen, Robert C.
  • Journal of Chemical Information and Computer Sciences, Vol. 44, Issue 1
  • DOI: 10.1021/ci034207y

Fragment Informatics and Computational Fragment-Based Drug Design: An Overview and Update: FRAGMENT INFORMATICS AND COMPUTATIONAL FBDD
journal, March 2012

  • Sheng, Chunquan; Zhang, Wannian
  • Medicinal Research Reviews, Vol. 33, Issue 3
  • DOI: 10.1002/med.21255

Identification of small molecule inhibitors of botulinum neurotoxin serotype E via footprint similarity
journal, October 2016

  • Zhou, Yuchen; McGillick, Brian E.; Teng, Yu-Han Gary
  • Bioorganic & Medicinal Chemistry, Vol. 24, Issue 20
  • DOI: 10.1016/j.bmc.2016.07.031

HIV-1 Envelope Glycoprotein Biosynthesis, Trafficking, and Incorporation
journal, July 2011

  • Checkley, Mary Ann; Luttge, Benjamin G.; Freed, Eric O.
  • Journal of Molecular Biology, Vol. 410, Issue 4
  • DOI: 10.1016/j.jmb.2011.04.042

Insights into the mechanism of HIV-1 envelope induced membrane fusion as revealed by its inhibitory peptides
journal, January 2011


Footprint-based identification of viral entry inhibitors targeting HIVgp41
journal, April 2012

  • Holden, Patrick M.; Kaur, Harmeet; Goyal, Rashi
  • Bioorganic & Medicinal Chemistry Letters, Vol. 22, Issue 8
  • DOI: 10.1016/j.bmcl.2012.02.017

LiGen: A High Performance Workflow for Chemistry Driven de Novo Design
journal, May 2013

  • Beccari, Andrea R.; Cavazzoni, Carlo; Beato, Claudia
  • Journal of Chemical Information and Modeling, Vol. 53, Issue 6
  • DOI: 10.1021/ci400078g

e-LEA3D: a computational-aided drug design web server
journal, May 2010


FOG: Fragment Optimized Growth Algorithm for the de Novo Generation of Molecules Occupying Druglike Chemical Space
journal, June 2009

  • Kutchukian, Peter S.; Lou, David; Shakhnovich, Eugene I.
  • Journal of Chemical Information and Modeling, Vol. 49, Issue 7
  • DOI: 10.1021/ci9000458

Integrating Medicinal Chemistry, Organic/Combinatorial Chemistry, and Computational Chemistry for the Discovery of Selective Estrogen Receptor Modulators with F orecaster , a Novel Platform for Drug Discovery
journal, December 2011

  • Therrien, Eric; Englebienne, Pablo; Arrowsmith, Andrew G.
  • Journal of Chemical Information and Modeling, Vol. 52, Issue 1
  • DOI: 10.1021/ci2004779

Development of Peptide and Small-Molecule HIV-1 Fusion Inhibitors that Target gp41
journal, September 2010


Staring off into chemical space
journal, August 2009


De Novo Fragment Design: A Medicinal Chemistry Approach to Fragment-Based Lead Generation
journal, March 2013

  • Talamas, Francisco X.; Ao-Ieong, Gloria; Brameld, Ken A.
  • Journal of Medicinal Chemistry, Vol. 56, Issue 7
  • DOI: 10.1021/jm4002605

Binding of antifusion peptides with HIVgp41 from molecular dynamics simulations: Quantitative correlation with experiment
journal, March 2007

  • Strockbine, Bentley; Rizzo, Robert C.
  • Proteins: Structure, Function, and Bioinformatics, Vol. 67, Issue 3
  • DOI: 10.1002/prot.21301

Docking Validation Resources: Protein Family and Ligand Flexibility Experiments
journal, October 2010

  • Mukherjee, Sudipto; Balius, Trent E.; Rizzo, Robert C.
  • Journal of Chemical Information and Modeling, Vol. 50, Issue 11
  • DOI: 10.1021/ci1001982

Automatic atom type and bond type perception in molecular mechanical calculations
journal, October 2006

  • Wang, Junmei; Wang, Wei; Kollman, Peter A.
  • Journal of Molecular Graphics and Modelling, Vol. 25, Issue 2
  • DOI: 10.1016/j.jmgm.2005.12.005

Receptor-Guided De Novo Design of Dengue Envelope Protein Inhibitors
journal, August 2015

  • Desai, Vishal H.; Kumar, Sivakumar Prasanth; Pandya, Himanshu A.
  • Applied Biochemistry and Biotechnology, Vol. 177, Issue 4
  • DOI: 10.1007/s12010-015-1784-y

Computer-aided design of non-nucleoside inhibitors of HIV-1 reverse transcriptase
journal, February 2006

  • Jorgensen, William L.; Ruiz-Caro, Juliana; Tirado-Rives, Julian
  • Bioorganic & Medicinal Chemistry Letters, Vol. 16, Issue 3
  • DOI: 10.1016/j.bmcl.2005.10.038

DOCK 6: Impact of new features and current docking performance
journal, April 2015

  • Allen, William J.; Balius, Trent E.; Mukherjee, Sudipto
  • Journal of Computational Chemistry, Vol. 36, Issue 15
  • DOI: 10.1002/jcc.23905

The Many Roles of Computation in Drug Discovery
journal, March 2004


Designing the molecular future
journal, November 2011


ZINC: A Free Tool to Discover Chemistry for Biology
journal, June 2012

  • Irwin, John J.; Sterling, Teague; Mysinger, Michael M.
  • Journal of Chemical Information and Modeling, Vol. 52, Issue 7
  • DOI: 10.1021/ci3001277

Structure-based de novo design and synthesis of aminothiazole-based p38 MAP kinase inhibitors
journal, September 2015

  • Park, Hwangseo; Lee, Soyoung; Hong, Sungwoo
  • Bioorganic & Medicinal Chemistry Letters, Vol. 25, Issue 18
  • DOI: 10.1016/j.bmcl.2015.07.094

Comparison of multiple Amber force fields and development of improved protein backbone parameters
journal, November 2006

  • Hornak, Viktor; Abel, Robert; Okur, Asim
  • Proteins: Structure, Function, and Bioinformatics, Vol. 65, Issue 3
  • DOI: 10.1002/prot.21123

Evaluation of DOCK 6 as a pose generation and database enrichment tool
journal, May 2012

  • Brozell, Scott R.; Mukherjee, Sudipto; Balius, Trent E.
  • Journal of Computer-Aided Molecular Design, Vol. 26, Issue 6
  • DOI: 10.1007/s10822-012-9565-y

Development and testing of a general amber force field
journal, January 2004

  • Wang, Junmei; Wolf, Romain M.; Caldwell, James W.
  • Journal of Computational Chemistry, Vol. 25, Issue 9
  • DOI: 10.1002/jcc.20035

Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method
journal, January 2000


Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation
journal, October 2002

  • Jakalian, Araz; Jack, David B.; Bayly, Christopher I.
  • Journal of Computational Chemistry, Vol. 23, Issue 16
  • DOI: 10.1002/jcc.10128

UCSF Chimera?A visualization system for exploratory research and analysis
journal, January 2004

  • Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C.
  • Journal of Computational Chemistry, Vol. 25, Issue 13
  • DOI: 10.1002/jcc.20084

Iterative partial equalization of orbital electronegativity—a rapid access to atomic charges
journal, January 1980


Potent suppression of HIV-1 replication in humans by T-20, a peptide inhibitor of gp41-mediated virus entry
journal, November 1998

  • Kilby, J. Michael; Hopkins, Sam; Venetta, Thomas M.
  • Nature Medicine, Vol. 4, Issue 11
  • DOI: 10.1038/3293

LEA3D: A Computer-Aided Ligand Design for Structure-Based Drug Design
journal, April 2005

  • Douguet, Dominique; Munier-Lehmann, Hélène; Labesse, Gilles
  • Journal of Medicinal Chemistry, Vol. 48, Issue 7
  • DOI: 10.1021/jm0492296

Virtual screening: an endless staircase?
journal, April 2010

  • Schneider, Gisbert
  • Nature Reviews Drug Discovery, Vol. 9, Issue 4
  • DOI: 10.1038/nrd3139

DOCK 6: Combining techniques to model RNA-small molecule complexes
journal, April 2009


Advances in multiparameter optimization methods for de novo drug design
journal, May 2014


HIV-1 Protease Inhibitors from Inverse Design in the Substrate Envelope Exhibit Subnanomolar Binding to Drug-Resistant Variants
journal, May 2008

  • Altman, Michael D.; Ali, Akbar; Kumar Reddy, G. S. Kiran
  • Journal of the American Chemical Society, Vol. 130, Issue 19
  • DOI: 10.1021/ja076558p

Structure-based de novo design, molecular docking and molecular dynamics of primaquine analogues acting as quinone reductase II inhibitors
journal, November 2015

  • Murce, Erika; Cuya-Guizado, Teobaldo Ricardo; Padilla-Chavarria, Helmut Isaac
  • Journal of Molecular Graphics and Modelling, Vol. 62
  • DOI: 10.1016/j.jmgm.2015.10.001

De Novo Drug Design Using Multiobjective Evolutionary Graphs
journal, January 2009

  • Nicolaou, Christos A.; Apostolakis, Joannis; Pattichis, Costas S.
  • Journal of Chemical Information and Modeling, Vol. 49, Issue 2
  • DOI: 10.1021/ci800308h

De Novo Design of Multitarget Ligands with an Iterative Fragment-Growing Strategy
journal, March 2014

  • Shang, Erchang; Yuan, Yaxia; Chen, Xinyi
  • Journal of Chemical Information and Modeling, Vol. 54, Issue 4
  • DOI: 10.1021/ci500021v

OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands
journal, September 2015

  • Chéron, Nicolas; Jasty, Naveen; Shakhnovich, Eugene I.
  • Journal of Medicinal Chemistry, Vol. 59, Issue 9
  • DOI: 10.1021/acs.jmedchem.5b00886

ZINC 15 – Ligand Discovery for Everyone
journal, November 2015

  • Sterling, Teague; Irwin, John J.
  • Journal of Chemical Information and Modeling, Vol. 55, Issue 11
  • DOI: 10.1021/acs.jcim.5b00559

Development and testing of a de novo drug-design algorithm
journal, October 2003


The Ecstasy and Agony of Assay Interference Compounds
journal, February 2017


SPROUT: A program for structure generation
journal, April 1993

  • Gillet, Valerie; Johnson, A. Peter; Mata, Pauline
  • Journal of Computer-Aided Molecular Design, Vol. 7, Issue 2
  • DOI: 10.1007/BF00126441

Open Babel: An open chemical toolbox
journal, October 2011

  • O'Boyle, Noel M.; Banck, Michael; James, Craig A.
  • Journal of Cheminformatics, Vol. 3, Issue 1
  • DOI: 10.1186/1758-2946-3-33

Similarity Searching of Chemical Databases Using Atom Environment Descriptors (MOLPRINT 2D):  Evaluation of Performance
journal, September 2004

  • Bender, Andreas; Mussa, Hamse Y.; Glen, Robert C.
  • Journal of Chemical Information and Computer Sciences, Vol. 44, Issue 5
  • DOI: 10.1021/ci0498719

Automated docking with grid-based energy evaluation
journal, May 1992

  • Meng, Elaine C.; Shoichet, Brian K.; Kuntz, Irwin D.
  • Journal of Computational Chemistry, Vol. 13, Issue 4
  • DOI: 10.1002/jcc.540130412

Generation and Selection of Novel Estrogen Receptor Ligands Using the De Novo Structure-Based Design Tool, SkelGen
journal, March 2006

  • Firth-Clark, Stuart; Willems, Henriëtte M. G.; Williams, Anthony
  • Journal of Chemical Information and Modeling, Vol. 46, Issue 2
  • DOI: 10.1021/ci0502956

Evidence that a prominent cavity in the coiled coil of HIV type 1 gp41 is an attractive drug target
journal, December 1998

  • Chan, D. C.; Chutkowski, C. T.; Kim, P. S.
  • Proceedings of the National Academy of Sciences, Vol. 95, Issue 26
  • DOI: 10.1073/pnas.95.26.15613

Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure
journal, April 1988

  • DesJarlais, Renee L.; Sheridan, Robert P.; Seibel, George L.
  • Journal of Medicinal Chemistry, Vol. 31, Issue 4
  • DOI: 10.1021/jm00399a006

The Properties of Known Drugs. 1. Molecular Frameworks
journal, January 1996

  • Bemis, Guy W.; Murcko, Mark A.
  • Journal of Medicinal Chemistry, Vol. 39, Issue 15
  • DOI: 10.1021/jm9602928

The computer program LUDI: A new method for the de novo design of enzyme inhibitors
journal, February 1992

  • B�hm, Hans-Joachim
  • Journal of Computer-Aided Molecular Design, Vol. 6, Issue 1
  • DOI: 10.1007/BF00124387

Identification of novel cannabinoid receptor ligandsvia evolutionary de novo design and rapid parallel synthesis
journal, July 2004

  • Rogers-Evans, Mark; Alanine, Alexander I.; Bleicher, Konrad H.
  • QSAR & Combinatorial Science, Vol. 23, Issue 6
  • DOI: 10.1002/qsar.200410012

Chemical space and biology
journal, December 2004


Pharmacophore-Based Similarity Scoring for DOCK
journal, August 2014

  • Jiang, Lingling; Rizzo, Robert C.
  • The Journal of Physical Chemistry B, Vol. 119, Issue 3
  • DOI: 10.1021/jp506555w

Navigating chemical space for biology and medicine
journal, December 2004


Virtual Screening for Bioactive Molecules by Evolutionary De Novo Design
journal, November 2000


Strategies for lead discovery: Application of footprint similarity targeting HIVgp41
journal, January 2014

  • Holden, Patrick M.; Allen, William J.; Gochin, Miriam
  • Bioorganic & Medicinal Chemistry, Vol. 22, Issue 1
  • DOI: 10.1016/j.bmc.2013.10.022

SHOP: Receptor-Based Scaffold HOPping by GRID-Based Similarity Searches
journal, February 2009

  • Bergmann, Rikke; Liljefors, Tommy; Sørensen, Morten D.
  • Journal of Chemical Information and Modeling, Vol. 49, Issue 3
  • DOI: 10.1021/ci800391v

Properties of Known Drugs. 2. Side Chains
journal, December 1999

  • Bemis, Guy W.; Murcko, Mark A.
  • Journal of Medicinal Chemistry, Vol. 42, Issue 25
  • DOI: 10.1021/jm9903996

Virtual screening of chemical libraries
journal, December 2004


Analysis of inhibitor binding in influenza virus neuraminidase
journal, April 2001


SMoG:  de Novo Design Method Based on Simple, Fast, and Accurate Free Energy Estimates. 1. Methodology and Supporting Evidence
journal, January 1996

  • DeWitte, Robert S.; Shakhnovich, Eugene I.
  • Journal of the American Chemical Society, Vol. 118, Issue 47
  • DOI: 10.1021/ja960751u

Biochemistry and Biophysics of HIV-1 gp41 - Membrane Interactions and Implications for HIV-1 Envelope Protein Mediated Viral-Cell Fusion and Fusion Inhibitor Design
journal, December 2011

  • Cai, Lifeng; Gochin, Miriam; Liu, Keliang
  • Current Topics in Medicinal Chemistry, Vol. 11, Issue 24
  • DOI: 10.2174/156802611798808497

Efficient Drug Lead Discovery and Optimization
journal, June 2009

  • Jorgensen, William L.
  • Accounts of Chemical Research, Vol. 42, Issue 6
  • DOI: 10.1021/ar800236t

Design, docking, and evaluation of multiple libraries against multiple targets
journal, January 2001


Chemical space
journal, December 2004

  • Kirkpatrick, Peter; Ellis, Clare
  • Nature, Vol. 432, Issue 7019
  • DOI: 10.1038/432823a

AutoGrow 3.0: An improved algorithm for chemically tractable, semi-automated protein inhibitor design
journal, July 2013

  • Durrant, Jacob D.; Lindert, Steffen; McCammon, J. Andrew
  • Journal of Molecular Graphics and Modelling, Vol. 44
  • DOI: 10.1016/j.jmgm.2013.05.006

LigBuilder 2: A Practical de Novo Drug Design Approach
journal, April 2011

  • Yuan, Yaxia; Pei, Jianfeng; Lai, Luhua
  • Journal of Chemical Information and Modeling, Vol. 51, Issue 5
  • DOI: 10.1021/ci100350u

Implementation of the Hungarian Algorithm to Account for Ligand Symmetry and Similarity in Structure-Based Design
journal, January 2014

  • Allen, William J.; Rizzo, Robert C.
  • Journal of Chemical Information and Modeling, Vol. 54, Issue 2
  • DOI: 10.1021/ci400534h

Inhibition of HIV Entry by Targeting the Envelope Transmembrane Subunit gp41
journal, March 2016


The Protein Data Bank
journal, January 2000


Grid-based molecular footprint comparison method for docking and de novo design: Application to HIVgp41
journal, February 2013

  • Balius, Trent E.; Allen, William J.; Mukherjee, Sudipto
  • Journal of Computational Chemistry, Vol. 34, Issue 14
  • DOI: 10.1002/jcc.23245

Similarity-based approaches to virtual screening
journal, June 2003


Critical evaluation of search algorithms for automated molecular docking and database screening
journal, July 1997


Ligand Pose and Orientational Sampling in Molecular Docking
journal, October 2013


LigBuilder: A Multi-Purpose Program for Structure-Based Drug Design
journal, August 2000

  • Wang, Renxiao; Gao, Ying; Lai, Luhua
  • Journal of Molecular Modeling, Vol. 6, Issue 7-8
  • DOI: 10.1007/s0089400060498

CONFIRM: connecting fragments found in receptor molecules
journal, July 2008

  • Thompson, David C.; Aldrin Denny, R.; Nilakantan, Ramaswamy
  • Journal of Computer-Aided Molecular Design, Vol. 22, Issue 10
  • DOI: 10.1007/s10822-008-9221-8

Discovery of a novel HCV helicase inhibitor by a de novo drug design approach
journal, June 2009

  • Kandil, Sahar; Biondaro, Sonia; Vlachakis, Dimitrios
  • Bioorganic & Medicinal Chemistry Letters, Vol. 19, Issue 11
  • DOI: 10.1016/j.bmcl.2009.04.074

Computer design of bioactive molecules: A method for receptor-based de novo ligand design
journal, December 1991

  • Moon, Joseph B.; Howe, W. Jeffrey
  • Proteins: Structure, Function, and Genetics, Vol. 11, Issue 4
  • DOI: 10.1002/prot.340110409

De novo design – hop(p)ing against hope
journal, December 2013


Computational Approaches for Fragment-Based and De Novo Design
journal, January 2010

  • Loving, Kathryn; Alberts, Ian; Sherman, Woody
  • Current Topics in Medicinal Chemistry, Vol. 10, Issue 1
  • DOI: 10.2174/156802610790232305