WatFinder: a ProDy tool for protein-water interactions

被引：0

作者：

Krieger, James M. ^{[1
]}

Doljanin, Frane ^{[2
,3
]}

Bogetti, Anthony T. ^{[4
]}

Zhang, Feng ^{[4
]}

Manivarma, Thiliban ^{[2
]}

Bahar, Ivet ^{[4
,5
]}

Mikulska-Ruminska, Karolina ^{[2
]}

机构：

[1] Natl Ctr Biotechnol CNB CSIC, Dept Macromol Struct, Biocomp Unit, Calle Darwin 3,Campus UAM Cantoblanco, Madrid 28049, Spain

[2] Nicolaus Copernicus Univ Torun, Inst Phys, Fac Phys Astron & Informat, Grudziadzka 5 St, PL-87100 Torun, Poland

[3] Univ Split, Fac Sci, Dept Phys, Split 21000, Croatia

[4] SUNY Stony Brook, Laufer Ctr Phys & Quantitat Biol, Stony Brook, NY 11794 USA

[5] SUNY Stony Brook, Renaissance Sch Med, Dept Biochem & Cell Biol, Stony Brook, NY 11794 USA

来源：

BIOINFORMATICS | 2024年 / 40卷 / 08期

基金：

欧盟地平线“2020”; 美国国家卫生研究院;

关键词：

MOLECULES;

D O I：

10.1093/bioinformatics/btae516

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

We introduce WatFinder, a tool designed to identify and visualize protein-water interactions (water bridges, water-mediated associations, or water channels, fluxes, and clusters) relevant to protein stability, dynamics, and function. WatFinder is integrated into ProDy, a Python API broadly used for structure-based prediction of protein dynamics. WatFinder provides a suite of functions for generating raw data as well as outputs from statistical analyses. The ProDy framework facilitates comprehensive automation and efficient analysis of the ensembles of structures resolved for a given protein or the time-evolved conformations from simulations in explicit water, as illustrated in five case studies presented in the Supplementary Material. Availability and implementation ProDy is open-source and freely available under MIT License from https://github.com/ProDy/ProDy.

引用

页数：4

共 15 条

[1] ProDy: Protein Dynamics Inferred from Theory and Experiments
Bakan, Ahmet
Meireles, Lidio M.
Bahar, Ivet
[J]. BIOINFORMATICS, 2011, 27 (11) : 1575 - 1577
[2] Function from structure? The crystal structure of human phosphatidylethanolamine-binding protein suggests a role in membrane signal transduction
Banfield, MJ
Barker, JJ
Perry, ACF
Brady, RL
[J]. STRUCTURE, 1998, 6 (10) : 1245 - 1254
[3] AquaMMapS: An Alternative Tool to Monitor the Role of Water Molecules During Protein-Ligand Association
Cuzzolin, Alberto
Deganutti, Giuseppe
Salmaso, Veronica
Sturlese, Mattia
Moro, Stefano
[J]. CHEMMEDCHEM, 2018, 13 (06) : 522 - 531
[4] OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
Eastman, Peter
Swails, Jason
Chodera, John D.
McGibbon, Robert T.
Zhao, Yutong
Beauchamp, Kyle A.
Wang, Lee-Ping
Simmonett, Andrew C.
Harrigan, Matthew P.
Stern, Chaya D.
Wiewiora, Rafal P.
Brooks, Bernard R.
Pande, Vijay S.
[J]. PLOS COMPUTATIONAL BIOLOGY, 2017, 13 (07)
[5] Inhibition of Low Molecular Weight Protein Tyrosine Phosphatase by an Induced-Fit Mechanism
He, Rongjun
Wang, Jifeng
Yu, Zhi-Hong
Zhang, Ruo-Yu
Liu, Sijiu
Wu, Li
Zhang, Zhong-Yin
[J]. JOURNAL OF MEDICINAL CHEMISTRY, 2016, 59 (19) : 9094 - 9106
[6] Just add water! The effect of water on the specificity of protein-ligand binding sites and its potential application to drug design
Ladbury, JE
[J]. CHEMISTRY & BIOLOGY, 1996, 3 (12): : 973 - 980
[7] GROMACS 3.0: a package for molecular simulation and trajectory analysis
Lindahl, E
Hess, B
van der Spoel, D
[J]. JOURNAL OF MOLECULAR MODELING, 2001, 7 (08) : 306 - 317
[8] WATCLUST: a tool for improving the design of drugs based on protein-water interactions
Lopez, Elias D.
Pablo Arcon, Juan
Gauto, Diego F.
Petruk, Ariel A.
Modenutti, Carlos P.
Dumas, Victoria G.
Marti, Marcelo A.
Turjanski, Adrian G.
[J]. BIOINFORMATICS, 2015, 31 (22) : 3697 - 3699
[9] Protein-water interactions in a dynamic world
Mattos, C
[J]. TRENDS IN BIOCHEMICAL SCIENCES, 2002, 27 (04) : 203 - 208
[10] Water in protein hydration and ligand recognition
Maurer, Manuela
Oostenbrink, Chris
[J]. JOURNAL OF MOLECULAR RECOGNITION, 2019, 32 (12)

← 1 2 →