No free energy lunch.

作者信息

Shoichet Brian K

机构信息

Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th Street, Suite 508D, San Francisco, California 94158-2330, USA.

出版信息

Nat Biotechnol. 2007 Oct;25(10):1109-10. doi: 10.1038/nbt1007-1109.

DOI:10.1038/nbt1007-1109

PMID:17921992

Abstract

摘要

相似文献

No free energy lunch.

Nat Biotechnol. 2007 Oct;25(10):1109-10. doi: 10.1038/nbt1007-1109.

A semiempirical free energy force field with charge-based desolvation.

J Comput Chem. 2007 Apr 30;28(6):1145-52. doi: 10.1002/jcc.20634.

Robust classification of "relevant" water molecules in putative protein binding sites.

J Med Chem. 2008 Feb 28;51(4):1063-7. doi: 10.1021/jm701023h. Epub 2008 Jan 31.

Protein-ligand binding free energy calculation by the Smooth Reaction Path Generation (SRPG) Method.

J Chem Inf Model. 2009 Aug;49(8):1944-51. doi: 10.1021/ci9002156.

Carbohydrate-binding proteins: Dissecting ligand structures through solvent environment occupancy.

J Phys Chem B. 2009 Jun 25;113(25):8717-24. doi: 10.1021/jp901196n.

Incorporating receptor flexibility in the molecular design of protein interfaces.

Protein Eng Des Sel. 2009 Sep;22(9):575-86. doi: 10.1093/protein/gzp042. Epub 2009 Jul 30.

Insights into activation and RNA binding of trp RNA-binding attenuation protein (TRAP) through all-atom simulations.

Proteins. 2008 Jun;71(4):1995-2011. doi: 10.1002/prot.21878.

Calculation of absolute protein-ligand binding constants with the molecular dynamics free energy perturbation method.

Methods Mol Biol. 2008;443:109-20. doi: 10.1007/978-1-59745-177-2_6.

Computation of the contribution from the cavity effect to protein-ligand binding free energy.

J Phys Chem B. 2008 Dec 4;112(48):15355-60. doi: 10.1021/jp8041439.

Multiple protonation equilibria in electrostatics of protein-protein binding.

J Phys Chem B. 2008 Nov 27;112(47):15074-85. doi: 10.1021/jp8029659.

引用本文的文献

Structure-based rational design of covalent probes.

Commun Chem. 2025 Aug 12;8(1):242. doi: 10.1038/s42004-025-01606-y.

Exploiting Solvent Exposed Salt-Bridge Interactions for the Discovery of Potent Inhibitors of SOS1 Using Free-Energy Perturbation Simulations.

ACS Med Chem Lett. 2025 Feb 28;16(3):444-453. doi: 10.1021/acsmedchemlett.4c00602. eCollection 2025 Mar 13.

Systematic analysis of the interactions driving small molecule-RNA recognition.

RSC Med Chem. 2020 Jun 4;11(7):802-813. doi: 10.1039/d0md00167h. eCollection 2020 Jul 1.

A systematic analysis of atomic protein-ligand interactions in the PDB.

Medchemcomm. 2017 Oct 1;8(10):1970-1981. doi: 10.1039/c7md00381a. Epub 2017 Sep 26.

Intimate connections: Inositol pyrophosphates at the interface of metabolic regulation and cell signaling.

J Cell Physiol. 2018 Mar;233(3):1897-1912. doi: 10.1002/jcp.26017. Epub 2017 Jun 15.

Implicit solvent methods for free energy estimation.

Eur J Med Chem. 2015 Feb 16;91:27-42. doi: 10.1016/j.ejmech.2014.08.064. Epub 2014 Aug 25.

Protein conformational switches: from nature to design.

Chemistry. 2012 Jun 25;18(26):7984-99. doi: 10.1002/chem.201200348. Epub 2012 Jun 11.

文献AI研究员

20分钟写一篇综述，助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型，支持多种主流文档格式。

立即体验