Research graph
References from Applications of water molecules for analysis of macromolecule properties. Local targets link to admitted publications; unresolved targets remain external evidence.
Unresolved reference
2002 · External reference
Roles for holes: are cavities in proteins mere packing defects?
2004 · External reference
10.1016/s0065-3233(08)60197-7
10.1016/s0065-3233(08)60197-7 · External reference
10.1016/j.bbagen.2016.05.036
10.1016/j.bbagen.2016.05.036 · External reference
The role of water molecules in the structure-based design of (5-hydroxynorvaline)-2-cyclosporin: synthesis, biological activity, and crystallographic analysis with cyclophilin A
10.1021/jm00017a020 · 1995 · External reference
10.1073/pnas.0307851100
10.1073/pnas.0307851100 · External reference
10.1098/rstb.2004.1498
10.1098/rstb.2004.1498 · External reference
Hydrogen and hydration in proteins
10.1385/cbb:40:3:351 · 2004 · External reference
10.1016/0076-6879(86)27014-7
10.1016/0076-6879(86)27014-7 · External reference
10.1016/0969-2126(93)90011-5
10.1016/0969-2126(93)90011-5 · External reference
10.1107/s0907444998012086
10.1107/s0907444998012086 · External reference
10.1093/nar/28.1.235
10.1093/nar/28.1.235 · External reference
Locating missing water molecules in protein cavities by the three-dimensional reference interaction site model theory of molecular solvation
10.1002/prot.21311 · 2006 · External reference
Theoretical study of the full reaction mechanism of human soluble epoxide hydrolase
10.1002/chem.200501519 · 2006 · External reference
Theoretical study of the reaction mechanism of phenolic acid decarboxylase
10.1111/febs.13525 · 2015 · External reference
Cation behavior in Faujasite zeolites upon water adsorption: a combination of Monte Carlo and molecular dynamics simulations
10.1021/jp902274t · 2009 · External reference
10.1155/2015/183918
10.1155/2015/183918 · External reference
10.1073/pnas.0400157101
10.1073/pnas.0400157101 · External reference
Virtual screening strategies in drug discovery: a critical review
10.2174/09298673113209990001 · 2013 · External reference
Protein-ligand docking in the new millennium – A retrospective of 10 years in the field
10.2174/0929867311320180002 · 2013 · External reference
10.1007/s12551-016-0247-1
10.1007/s12551-016-0247-1 · External reference
10.1002/prot.340120302
10.1002/prot.340120302 · External reference
10.1002/(sici)1097-0134(19980801)32:2<229::aid-prot9>3.0.co;2-f
10.1002/(sici)1097-0134(19980801)32:2<229::aid-prot9>3.0.co;2-f · External reference
10.1093/proeng/gzg001
10.1093/proeng/gzg001 · External reference
10.1002/pro.5560011203
10.1002/pro.5560011203 · External reference
10.1038/35102009
10.1038/35102009 · External reference
10.1021/bi026990d
10.1021/bi026990d · External reference
10.1016/s0959-440x(94)90178-3
10.1016/s0959-440x(94)90178-3 · External reference
10.1126/science.1948083
10.1126/science.1948083 · External reference
10.1021/ja403405d
10.1021/ja403405d · External reference
10.1021/ct500358r
10.1021/ct500358r · External reference
10.1371/journal.pone.0032036
10.1371/journal.pone.0032036 · External reference
Analysis of biomolecular solvation sites by 3D-RISM theory
10.1021/jp4046116 · 2013 · External reference
Optimal water networks in protein cavities with GAsol and 3D-RISM
10.1093/bioinformatics/bty024 · 2018 · External reference
10.1002/jcc.22984
10.1002/jcc.22984 · External reference
10.1093/bioinformatics/btu424
10.1093/bioinformatics/btu424 · External reference
Identification of conserved water sites in protein structures for drug design
10.1021/acs.jcim.7b00443 · 2017 · External reference
AutoDock Vina: IMPROVING the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
2009 · External reference
Dowser++, a new method of hydrating protein structures
10.1002/prot.25081 · 2016 · External reference
Water molecules in a protein cavity detected by a statistical−mechanical theory
10.1021/ja054434b · 2005 · External reference
Calculation of local water densities in biological systems: a comparison of molecular dynamics simulations and the 3D-RISM-KH molecular theory of solvation
10.1021/jp102587q · 2011 · External reference
Towards a universal method for calculating hydration free energies: a 3D reference interaction site model with partial molar volume correction
2010 · External reference
3D-RISM-Dock: A new fragment-based drug design protocol
10.1021/ct300257v · 2012 · External reference
10.1021/ct4009359
10.1021/ct4009359 · External reference
ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment
10.1093/bioinformatics/btq100 · 2010 · External reference
The protein data bank: a computer-based archival file for macromolecular structures
10.1016/s0022-2836(77)80200-3 · 1977 · External reference
10.1371/journal.pone.0172743
10.1371/journal.pone.0172743 · External reference
10.3390/ijms17020144
10.3390/ijms17020144 · External reference
10.1038/s41467-018-05769-2
10.1038/s41467-018-05769-2 · External reference
10.1021/ci6003527
10.1021/ci6003527 · External reference
Structural and dynamic properties of water around acetylcholinesterase
10.1110/ps.0214002 · 2009 · External reference
Large-scale study of hydration environments through hydration sites
10.1021/acs.jpcb.9b02490 · 2019 · External reference
A direct measure of the contribution of solvent reorganization to the enthalpy of binding
10.1021/ja00102a021 · 1994 · External reference
10.3109/10799899709036621
10.3109/10799899709036621 · External reference
10.2174/156802610790232288
10.2174/156802610790232288 · External reference
AutoDock-GIST: incorporating thermodynamics of active-site water into scoring function for accurate protein-ligand docking
10.3390/molecules21111604 · 2016 · External reference
A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
10.1021/jm00145a002 · 1985 · External reference
10.1006/jmbi.1996.0746
10.1006/jmbi.1996.0746 · External reference
10.1007/s00894-003-0129-x
10.1007/s00894-003-0129-x · External reference
10.1021/ci200150p
10.1021/ci200150p · External reference
10.1016/s0223-5234(00)00167-7
10.1016/s0223-5234(00)00167-7 · External reference
Modelling of solvent positions around polar groups in proteins
10.1093/protein/4.5.531 · 1991 · External reference
AQUARIUS2: knowledge-based modeling of solvent sites around proteins
10.1002/jcc.540140902 · 1993 · External reference
Inhomogeneous fluid approach to solvation thermodynamics. 1. Theory
10.1021/jp9723574 · 1998 · External reference
Assessing the accuracy of inhomogeneous fluid solvation theory in predicting hydration free energies of simple solutes
10.1021/jp4042233 · 2013 · External reference
Hydration thermodynamic properties of amino acid analogues: a systematic comparison of biomolecular force fields and water models
10.1021/jp0641029 · 2006 · External reference
Calculating water thermodynamics in the binding site of proteins – applications of WaterMap to drug discovery
10.2174/1568026617666170414141452 · 2017 · External reference
Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST
10.1002/jcc.24417 · 2016 · External reference
WATCLUST: a tool for improving the design of drugs based on protein-water interactions: Fig. 1
10.1093/bioinformatics/btv411 · 2015 · External reference
10.1007/978-1-61779-465-0_24
10.1007/978-1-61779-465-0_24 · External reference
WATsite: hydration site prediction program with PyMOL interface
10.1002/jcc.23616 · 2014 · External reference
10.1002/jcc.20751
10.1002/jcc.20751 · External reference
10.1021/ci600253e
10.1021/ci600253e · External reference
High end GPCR design: crafted ligand design and druggability analysis using protein structure, lipophilic hotspots and explicit water networks
10.1186/2193-9616-1-23 · 2013 · External reference
10.1021/ci500746d
10.1021/ci500746d · External reference
Unresolved reference
External reference
10.1021/jp9047456
10.1021/jp9047456 · External reference
WScore: A Flexible and Accurate Treatment of Explicit Water Molecules in Ligand-Receptor Docking
10.1021/acs.jmedchem.6b00131 · 2016 · External reference
AQUA-DUCT: a ligands tracking tool
10.1093/bioinformatics/btx125 · 2017 · External reference
AQUA-DUCT 1.0: structural and functional analysis of macromolecules from an intramolecular voids perspective
2019 · External reference
10.1021/acs.jctc.7b00592
10.1021/acs.jctc.7b00592 · External reference
A water-swap reaction coordinate for the calculation of absolute protein–ligand binding free energies
10.1063/1.3519057 · 2011 · External reference
10.1021/ci500571h
10.1021/ci500571h · External reference
10.1021/ct400711g
10.1021/ct400711g · External reference
10.1002/cmdc.201700564
10.1002/cmdc.201700564 · External reference
Unresolved reference
External reference
Molecular modeling of organic and biomolecular systems using BOSS and MCPRO
10.1002/jcc.20297 · 2005 · External reference
Exploring Solanum tuberosum epoxide hydrolase internal architecture by water molecules tracking
10.3390/biom8040143 · 2018 · External reference
10.1517/17460441.2013.749853
10.1517/17460441.2013.749853 · External reference
10.1016/j.biotechadv.2012.02.002
10.1016/j.biotechadv.2012.02.002 · External reference
10.1021/cr300384w
10.1021/cr300384w · External reference
Protein hydration dynamics in aqueous solution
10.1039/fd9960300227 · 1996 · External reference
Distant Non-obvious mutations influence the activity of a hyperthermophilic Pyrococcus furiosus phosphoglucose isomerase
10.3390/biom9060212 · 2019 · External reference
10.1021/acscatal.6b02081
10.1021/acscatal.6b02081 · External reference
Molecular dynamics simulations reveal structural differences among allelic variants of membrane-anchored cytochrome P450 2D6
10.1021/acs.jcim.8b00080 · 2018 · External reference
Analysis of water channels by molecular dynamics simulation of heterotetrameric sarcosine oxidase
10.2142/biophysico.12.0_131 · 2015 · External reference
MOLE 2.0: advanced approach for analysis of biomacromolecular channels
10.1186/1758-2946-5-39 · 2013 · External reference
10.1371/journal.pcbi.1002708
10.1371/journal.pcbi.1002708 · External reference
10.1093/bioinformatics/btu364
10.1093/bioinformatics/btu364 · External reference
10.1093/bioinformatics/bty386
10.1093/bioinformatics/bty386 · External reference
10.1109/isvd.2012.25
10.1109/isvd.2012.25 · 2012 · External reference
CAVER: algorithms for analyzing dynamics of tunnels in macromolecules
10.1109/tcbb.2015.2459680 · 2016 · External reference
Computing cavities, channels, pores and pockets in proteins from non-spherical ligands models
10.1093/bioinformatics/btt644 · 2014 · External reference
10.1111/j.1467-8659.2008.01227.x
10.1111/j.1467-8659.2008.01227.x · External reference
10.1021/bi901900s
10.1021/bi901900s · External reference
10.1021/acsomega.7b01084
10.1021/acsomega.7b01084 · External reference
Solvent flux method (SFM): a case study of water access to Candida antarctica lipase B
10.1021/ct500791e · 2014 · External reference
10.1021/ct401098b
10.1021/ct401098b · External reference
Exploring the entry route of palmitic acid and palmitoylcarnitine into myoglobin
10.1016/j.abb.2018.07.024 · 2018 · External reference
Unresolved reference
External reference
Modulating D-amino acid oxidase (DAAO) substrate specificity through facilitated solvent access
10.1371/journal.pone.0198990 · 2018 · External reference
10.1021/acs.jpcb.8b03842
10.1021/acs.jpcb.8b03842 · External reference
Watergate: visual exploration of water trajectories in protein dynamics
2017 · External reference
10.1039/c8sm01483c
10.1039/c8sm01483c · External reference
10.1007/s10822-017-0016-7
10.1007/s10822-017-0016-7 · External reference
Modeling of glycidoxypropyltrimethoxy silane compositions using molecular dynamics simulations
10.1016/j.commatsci.2017.08.033 · 2017 · External reference
10.3390/ijms19092588
10.3390/ijms19092588 · External reference
10.3390/molecules23102616
10.3390/molecules23102616 · External reference
10.1002/cphc.201601327
10.1002/cphc.201601327 · External reference
The role of hydrophobicity in the cold denaturation of proteins under high pressure: a study on apomyoglobin
10.1063/1.5080942 · 2019 · External reference
Role of structural ions on the dynamics of the Pseudomonas fluorescens 07A metalloprotease
10.1016/j.foodchem.2019.01.204 · 2019 · External reference
10.1371/journal.pcbi.1006284
10.1371/journal.pcbi.1006284 · External reference
Effects of surface crack on the mechanical properties of Silica: a molecular dynamics simulation study
10.1016/j.engfracmech.2018.12.025 · 2019 · External reference
Computational insight into the structural organization of full-length toll-like receptor 4 dimer in a model phospholipid bilayer
10.3389/fimmu.2018.00489 · 2018 · External reference
Potential role of salt-bridges in the hinge-like movement of apicomplexa specific β-hairpin of Plasmodium and Toxoplasma profilins: A molecular dynamics simulation study
10.1002/jcb.26579 · 2018 · External reference
10.1021/acs.jpcb.6b09900
10.1021/acs.jpcb.6b09900 · External reference
10.1016/j.jhazmat.2018.05.042
10.1016/j.jhazmat.2018.05.042 · External reference
10.1021/acschembio.8b00231
10.1021/acschembio.8b00231 · External reference
Understanding enzymatic degradation of single-walled carbon nanotubes triggered by functionalization using molecular dynamics simulation
10.1039/c7en00050b · 2017 · External reference
10.1074/jbc.ra118.002441
10.1074/jbc.ra118.002441 · External reference
10.1038/s41564-019-0481-y
10.1038/s41564-019-0481-y · External reference
Molecular basis for the maintenance of lipid asymmetry in the outer membrane of Escherichia coli
2017 · External reference
Insights into the ion-coupling mechanism in the MATE transporter NorM-VC
10.1088/1478-3975/aa5ee7 · 2017 · External reference
10.1021/acs.jpcb.7b12095
10.1021/acs.jpcb.7b12095 · External reference
Structure, function and dynamics in acyl carrier proteins
10.1371/journal.pone.0219435 · 2019 · External reference
10.1016/j.bpj.2009.08.031
10.1016/j.bpj.2009.08.031 · External reference
10.1021/jacs.9b06275
10.1021/jacs.9b06275 · External reference
10.1002/anie.201402087
10.1002/anie.201402087 · External reference
10.1039/c8cp04118k
10.1039/c8cp04118k · External reference
Prediction of small molecule hydration thermodynamics with grid cell theory
10.1021/ct400783h · 2014 · External reference
10.1038/nmeth.4067
10.1038/nmeth.4067 · External reference
10.1021/ct2007814
10.1021/ct2007814 · External reference
