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There are 12228 results for: content related to: Embracing Protein Plasticity in Ligand Docking

  1. Structure and Modeling of GPCRs: Implications for Drug Discovery

    GPCR Molecular Pharmacology and Drug Targeting: Shifting Paradigms and New Directions

    Kimberly A. Reynolds, Vsevolod Katritch, Ruben Abagyan, Pages: 385–433, 2010

    Published Online : 15 JUL 2010, DOI: 10.1002/9780470627327.ch15

  2. Identifying ligands at orphan GPCRs: current status using structure-based approaches

    British Journal of Pharmacology

    Tony Ngo, Irina Kufareva, James LJ Coleman, Robert M Graham, Ruben Abagyan and Nicola J Smith

    Version of Record online : 5 MAR 2016, DOI: 10.1111/bph.13452

  3. Homology modeling with internal coordinate mechanics: Deformation zone mapping and improvements of models via conformational search

    Proteins: Structure, Function, and Bioinformatics

    Volume 29, Issue S1, 1997, Pages: 29–37, Ruben Abagyan, Serge Batalov, Timothy Cardozo, Maxim Totrov, Jeremy Webber and Yingyao Zhou

    Version of Record online : 7 DEC 1998, DOI: 10.1002/(SICI)1097-0134(1997)1+<29::AID-PROT5>3.0.CO;2-J

  4. Flexible protein–ligand docking by global energy optimization in internal coordinates

    Proteins: Structure, Function, and Bioinformatics

    Volume 29, Issue S1, 1997, Pages: 215–220, Maxim Totrov and Ruben Abagyan

    Version of Record online : 7 DEC 1998, DOI: 10.1002/(SICI)1097-0134(1997)1+<215::AID-PROT29>3.0.CO;2-Q

  5. The Human Pocketome

    De novo Molecular Design

    Ruben Abagyan, Clarisse Gravina Ricci, Pages: 79–96, 2013

    Published Online : 11 OCT 2013, DOI: 10.1002/9783527677016.ch3

  6. A new method for modeling large-scale rearrangements of protein domains

    Proteins: Structure, Function, and Bioinformatics

    Volume 27, Issue 3, March 1997, Pages: 410–424, Vladimir Maiorov and Ruben Abagyan

    Version of Record online : 7 DEC 1998, DOI: 10.1002/(SICI)1097-0134(199703)27:3<410::AID-PROT9>3.0.CO;2-G

  7. Docking and Scoring in Drug Discovery

    Standard Article

    Burger's Medicinal Chemistry and Drug Discovery

    Francesca Spyrakis, Pietro Cozzini and Glen Eugene Kellogg

    Published Online : 15 SEP 2010, DOI: 10.1002/0471266949.bmc140

  8. GPCR 3D homology models for ligand screening: Lessons learned from blind predictions of adenosine A2a receptor complex

    Proteins: Structure, Function, and Bioinformatics

    Volume 78, Issue 1, January 2010, Pages: 197–211, Vsevolod Katritch, Manuel Rueda, Polo Chun-Hung Lam, Mark Yeager and Ruben Abagyan

    Version of Record online : 19 JUN 2009, DOI: 10.1002/prot.22507

  9. Virtual Ligand Screening Against Comparative Models of Proteins

    Proteins in Solution and at Interfaces: Methods and Applications in Biotechnology and Materials Science

    Juan M. Ruso, Ángel Piñeiro, Pages: 179–191, 2013

    Published Online : 5 MAR 2013, DOI: 10.1002/9781118523063.ch8

  10. Challenges and advances in computational docking: 2009 in review

    Journal of Molecular Recognition

    Volume 24, Issue 2, March/April 2011, Pages: 149–164, Elizabeth Yuriev, Mark Agostino and Paul A. Ramsland

    Version of Record online : 23 OCT 2010, DOI: 10.1002/jmr.1077

  11. Prediction of the binding energy for small molecules, peptides and proteins

    Journal of Molecular Recognition

    Volume 12, Issue 3, May/June 1999, Pages: 177–190, Matthieu Schapira, Maxim Totrov and Ruben Abagyan

    Version of Record online : 14 JUN 1999, DOI: 10.1002/(SICI)1099-1352(199905/06)12:3<177::AID-JMR451>3.0.CO;2-Z

  12. You have free access to this content
    Soft protein–protein docking in internal coordinates

    Protein Science

    Volume 11, Issue 2, February 2002, Pages: 280–291, Juan Fernández-Recio, Maxim Totrov and Ruben Abagyan

    Version of Record online : 13 APR 2009, DOI: 10.1110/ps.19202

  13. Outstanding challenges in protein–ligand docking and structure-based virtual screening

    Wiley Interdisciplinary Reviews: Computational Molecular Science

    Volume 1, Issue 2, March/April 2011, Pages: 229–259, Bohdan Waszkowycz, David E. Clark and Emanuela Gancia

    Version of Record online : 16 MAR 2011, DOI: 10.1002/wcms.18

  14. Receptor flexibility in small-molecule docking calculations

    Wiley Interdisciplinary Reviews: Computational Molecular Science

    Volume 1, Issue 2, March/April 2011, Pages: 298–314, Daria B. Kokh, Rebecca C. Wade and Wolfgang Wenzel

    Version of Record online : 17 MAR 2011, DOI: 10.1002/wcms.29

  15. ICFF: A new method to incorporate implicit flexibility into an internal coordinate force field

    Journal of Computational Chemistry

    Volume 24, Issue 2, 30 January 2003, Pages: 254–265, Vsevolod Katritch, Maxim Totrov and Ruben Abagyan

    Version of Record online : 19 DEC 2002, DOI: 10.1002/jcc.10091

  16. Molecular basis for the binding polyspecificity of an anti-cholera toxin peptide 3 monoclonal antibody

    Journal of Molecular Recognition

    Volume 19, Issue 1, January/February 2006, Pages: 49–59, Livia Otte, Tobias Knaute, Jens Schneider-Mergener and Achim Kramer

    Version of Record online : 7 NOV 2005, DOI: 10.1002/jmr.757

  17. Homology modeling by the ICM method

    Proteins: Structure, Function, and Bioinformatics

    Volume 23, Issue 3, November 1995, Pages: 403–414, Timothy Cardozo, Maxim Totrov and Ruben Abagyan

    Version of Record online : 3 FEB 2004, DOI: 10.1002/prot.340230314

  18. ICM-DISCO docking by global energy optimization with fully flexible side-chains

    Proteins: Structure, Function, and Bioinformatics

    Volume 52, Issue 1, 1 July 2003, Pages: 113–117, Juan Fernández-Recio, Maxim Totrov and Ruben Abagyan

    Version of Record online : 14 MAY 2003, DOI: 10.1002/prot.10383

  19. You have free access to this content
    Structural Determinants of PERK Inhibitor Potency and Selectivity

    Chemical Biology & Drug Design

    Volume 76, Issue 6, December 2010, Pages: 480–495, Hong Wang, Jaime Blais, David Ron and Timothy Cardozo

    Version of Record online : 11 NOV 2010, DOI: 10.1111/j.1747-0285.2010.01048.x

  20. Efficient parallelization of the energy, surface, and derivative calculations for internal coordinate mechanics

    Journal of Computational Chemistry

    Volume 15, Issue 10, October 1994, Pages: 1105–1112, Maxim Totrov and Ruben Abagyan

    Version of Record online : 7 SEP 2004, DOI: 10.1002/jcc.540151006