| review article | Q7318358 |
| scholarly article | Q13442814 |
| P2093 | author name string | Karolina Mitusińska | |
| Weronika Bagrowska | |||
| Agata Raczyńska | |||
| Artur Góra | |||
| Maria Bzówka | |||
| P2860 | cites work | Chemistry of ion coordination and hydration revealed by a K+ channel-Fab complex at 2.0 A resolution | Q22337277 |
| The Protein Data Bank | Q24515306 | ||
| Insights into Protein-Ligand Interactions: Mechanisms, Models, and Methods | Q26773062 | ||
| Molecular dynamics, monte carlo simulations, and langevin dynamics: a computational review | Q27012799 | ||
| Buried water molecules contribute to the conformational stability of a protein | Q27640733 | ||
| MOLE 2.0: advanced approach for analysis of biomacromolecular channels | Q27703086 | ||
| The role of water molecules in the structure-based design of (5-hydroxynorvaline)-2-cyclosporin: synthesis, biological activity, and crystallographic analysis with cyclophilin A | Q27729830 | ||
| Role of water in plasticity, stability, and action of proteins: the crystal structures of lysozyme at very low levels of hydration | Q27765158 | ||
| AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading | Q27860652 | ||
| The Protein Data Bank: a computer-based archival file for macromolecular structures | Q27860989 | ||
| Rapid and accurate prediction and scoring of water molecules in protein binding sites | Q28481339 | ||
| CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures | Q28484476 | ||
| Water in protein structure prediction | Q30339048 | ||
| Locating missing water molecules in protein cavities by the three-dimensional reference interaction site model theory of molecular solvation. | Q30358933 | ||
| PyWATER: a PyMOL plug-in to find conserved water molecules in proteins by clustering. | Q30364296 | ||
| Evaluating Free Energies of Binding and Conservation of Crystallographic Waters Using SZMAP. | Q30376731 | ||
| Solvent Flux Method (SFM): A Case Study of Water Access to Candida antarctica Lipase B. | Q30381557 | ||
| Hydration of proteins and nucleic acids: Advances in experiment and theory. A review. | Q30388707 | ||
| CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules | Q30389235 | ||
| Theoretical Study of the Full Reaction Mechanism of Human Soluble Epoxide Hydrolase | Q62556676 | ||
| Exploring Solanum tuberosum Epoxide Hydrolase Internal Architecture by Water Molecules Tracking. | Q64952050 | ||
| Analysis of ligand-bound water molecules in high-resolution crystal structures of protein-ligand complexes. | Q64977617 | ||
| Protein hydration in aqueous solution | Q68053669 | ||
| Determination of water structure around biomolecules using X-ray and neutron diffraction methods | Q69576069 | ||
| Energetic and entropic factors determining binding affinity in protein-ligand complexes | Q73065382 | ||
| Protein hydration dynamics in aqueous solution | Q73309229 | ||
| How many water molecules can be detected by protein crystallography? | Q74629747 | ||
| Hydration thermodynamic properties of amino acid analogues: a systematic comparison of biomolecular force fields and water models | Q80189502 | ||
| Water molecules in a protein cavity detected by a statistical-mechanical theory | Q81427075 | ||
| Computing the thermodynamic contributions of interfacial water | Q83065308 | ||
| WATCLUST: a tool for improving the design of drugs based on protein-water interactions | Q85638976 | ||
| Partial Intrinsic Disorder Governs the Dengue Capsid Protein Conformational Ensemble | Q88788400 | ||
| Effect of surfactants on the interaction of phenol with laccase: Molecular docking and molecular dynamics simulation studies | Q88958167 | ||
| Self-Assembly Simulations of Classic Claudins-Insights into the Pore Structure, Selectivity, and Higher Order Complexes | Q88993715 | ||
| WScore: A Flexible and Accurate Treatment of Explicit Water Molecules in Ligand-Receptor Docking | Q89138839 | ||
| Water Networks Can Determine the Affinity of Ligand Binding to Proteins | Q90093755 | ||
| Exploring the entry route of palmitic acid and palmitoylcarnitine into myoglobin | Q90854042 | ||
| Mechanics and nanovoid nucleation dynamics: effects of polar functionality in glassy polymer networks | Q91411917 | ||
| Large-Scale Study of Hydration Environments through Hydration Sites | Q91538790 | ||
| Structure, function and dynamics in acyl carrier proteins | Q91768411 | ||
| The role of hydrophobicity in the cold denaturation of proteins under high pressure: A study on apomyoglobin | Q91839713 | ||
| Role of structural ions on the dynamics of the Pseudomonas fluorescens 07A metalloprotease | Q92083243 | ||
| AQUA-DUCT 1.0: structural and functional analysis of macromolecules from an intramolecular voids perspective | Q92147088 | ||
| Distant Non-Obvious Mutations Influence the Activity of a Hyperthermophilic Pyrococcus furiosus Phosphoglucose Isomerase | Q92494026 | ||
| MD Simulations Reveal Complex Water Paths in Squalene-Hopene Cyclase: Tunnel-Obstructing Mutations Increase the Flow of Water in the Active Site | Q92926902 | ||
| Evidence for phospholipid export from the bacterial inner membrane by the Mla ABC transport system | Q93001418 | ||
| A computational procedure for determining energetically favorable binding sites on biologically important macromolecules | Q30406755 | ||
| Predicting conserved water-mediated and polar ligand interactions in proteins using a K-nearest-neighbors genetic algorithm. | Q30426491 | ||
| Prediction of the water content in protein binding sites | Q30495095 | ||
| Transient access to the protein interior: simulation versus NMR. | Q30626640 | ||
| ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment | Q33808336 | ||
| Hydrophobicity: is LogP(o/w) more than the sum of its parts? | Q34014544 | ||
| Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements | Q34285601 | ||
| Dipole Moment and Binding Energy of Water in Proteins from Crystallographic Analysis | Q34337377 | ||
| Molecular modeling of organic and biomolecular systems using BOSS and MCPRO. | Q34456227 | ||
| CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures. | Q35176321 | ||
| Water-protein interactions from high-resolution protein crystallography | Q35214098 | ||
| Internal water molecules and H‐bonding in biological macromolecules: A review of structural features with functional implications | Q35222975 | ||
| Hydrogen and hydration in proteins | Q35813607 | ||
| Roles for holes: are cavities in proteins mere packing defects? | Q35882415 | ||
| Calculation of local water densities in biological systems: a comparison of molecular dynamics simulations and the 3D-RISM-KH molecular theory of solvation | Q36124795 | ||
| Waterdock 2.0: Water placement prediction for Holo-structures with a pymol plugin | Q36290001 | ||
| Calculating Water Thermodynamics in the Binding Site of Proteins - Applications of WaterMap to Drug Discovery | Q36348140 | ||
| Water and proteins: a love-hate relationship | Q37072904 | ||
| Gates of enzymes | Q37098498 | ||
| The role of water molecules in computational drug design | Q37636270 | ||
| A Cavity Corrected 3D-RISM Functional for Accurate Solvation Free Energies | Q37636706 | ||
| Protein hydration and function | Q37778378 | ||
| Software tools for identification, visualization and analysis of protein tunnels and channels. | Q37986301 | ||
| Approaches to efficiently estimate solvation and explicit water energetics in ligand binding: the use of WaterMap | Q38071408 | ||
| Protein-ligand docking in the new millennium--a retrospective of 10 years in the field | Q38093314 | ||
| Virtual screening strategies in drug discovery: a critical review. | Q38104785 | ||
| Structural and dynamic properties of water around acetylcholinesterase | Q38269746 | ||
| Allosteric modulation model of the mu opioid receptor by herkinorin, a potent not alkaloidal agonist | Q38736870 | ||
| AQUA-DUCT a ligands tracking tool. | Q38882976 | ||
| Software for molecular docking: a review. | Q39310583 | ||
| Dowser++, a new method of hydrating protein structures | Q39702497 | ||
| 3D-RISM-Dock: A New Fragment-Based Drug Design Protocol | Q40276857 | ||
| SPAM: A Simple Approach for Profiling Bound Water Molecules | Q40291869 | ||
| CHARMM36m: an improved force field for folded and intrinsically disordered proteins | Q40299880 | ||
| Prediction of Small Molecule Hydration Thermodynamics with Grid Cell Theory. | Q40309053 | ||
| Water: now you see it, now you don't | Q40700389 | ||
| Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST. | Q41339143 | ||
| Analysis of water channels by molecular dynamics simulation of heterotetrameric sarcosine oxidase. | Q42185283 | ||
| Assessing the accuracy of inhomogeneous fluid solvation theory in predicting hydration free energies of simple solutes | Q42213043 | ||
| WATsite: hydration site prediction program with PyMOL interface | Q42407198 | ||
| Multiple molecular dynamics simulations of TEM beta-lactamase: dynamics and water binding of the omega-loop | Q42602812 | ||
| Solvent structure in crystals of trypsin determined by X-ray and neutron diffraction | Q44121797 | ||
| Structural changes of water in the Schiff base region of bacteriorhodopsin: proposal of a hydration switch model. | Q44324229 | ||
| WATGEN: an algorithm for modeling water networks at protein-protein interfaces. | Q46028266 | ||
| Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories. | Q46202746 | ||
| APICOMPLEXA SPECIFIC β-HAIRPIN OF PLASMODIUM AND TOXOPLASMA PROFILINS: A MOLECULAR DYNAMICS SIMULATION STUDY. | Q46242214 | ||
| Computing cavities, channels, pores and pockets in proteins from non-spherical ligands models. | Q46893087 | ||
| Entropy is key to the formation of pentacyclic terpenoids by enzyme-catalyzed polycyclization | Q46908495 | ||
| AquaMMapS: an alternative tool to monitor the role of water molecules during protein-ligand association. | Q47342876 | ||
| Identification of Conserved Water Sites in Protein Structures for Drug Design. | Q47384926 | ||
| Optimal water networks in protein cavities with GAsol and 3D-RISM. | Q47561007 | ||
| Toward Understanding the Molecular Recognition of Albumin by p53-Activating Stapled Peptide ATSP-7041. | Q48099713 | ||
| WaterScore: a novel method for distinguishing between bound and displaceable water molecules in the crystal structure of the binding site of protein-ligand complexes. | Q48556382 | ||
| Tracking the flow of water through photosystem II using molecular dynamics and streamline tracing. | Q48825828 | ||
| Time-averaged distributions of solute and solvent motions: exploring proton wires of GFP and PfM2DH. | Q50445828 | ||
| Analysis of biomolecular solvation sites by 3D-RISM theory. | Q50992568 | ||
| Insights into the ion-coupling mechanism in the MATE transporter NorM-VC. | Q51014638 | ||
| Characterizing Structural Stability of Amyloid Motif Fibrils Mediated by Water Molecules. | Q51017813 | ||
| Efficient Characterization of Protein Cavities within Molecular Simulation Trajectories: trj_cavity. | Q51088716 | ||
| AutoDock-GIST: Incorporating Thermodynamics of Active-Site Water into Scoring Function for Accurate Protein-Ligand Docking. | Q51304233 | ||
| Placevent: an algorithm for prediction of explicit solvent atom distribution-application to HIV-1 protease and F-ATP synthase. | Q51377144 | ||
| AcquaAlta: a directional approach to the solvation of ligand-protein complexes. | Q51552985 | ||
| Towards a universal method for calculating hydration free energies: a 3D reference interaction site model with partial molar volume correction. | Q51591551 | ||
| A water-swap reaction coordinate for the calculation of absolute protein-ligand binding free energies. | Q51605124 | ||
| A common reference framework for analyzing/comparing proteins and ligands. Fingerprints for Ligands and Proteins (FLAP): theory and application. | Q51919227 | ||
| Computational Insight Into the Structural Organization of Full-Length Toll-Like Receptor 4 Dimer in a Model Phospholipid Bilayer. | Q52338692 | ||
| Modelling of solvent positions around polar groups in proteins. | Q52448779 | ||
| Role of the Bound Phospholipids in the Structural Stability of Cholesteryl Ester Transfer Protein. | Q52690275 | ||
| Theoretical study of the reaction mechanism of phenolic acid decarboxylase. | Q52914223 | ||
| Modulating D-amino acid oxidase (DAAO) substrate specificity through facilitated solvent access. | Q55283538 | ||
| Interaction of the human erythrocyte Band 3 anion exchanger 1 (AE1, SLC4A1) with lipids and glycophorin A: Molecular organization of the Wright (Wr) blood group antigen | Q56333675 | ||
| Effective lead optimization targeting the displacement of bridging receptor-ligand water molecules | Q56977007 | ||
| The architecture of the OmpC-MlaA complex sheds light on the maintenance of outer membrane lipid asymmetry in | Q57114421 | ||
| Molecular Dynamics Simulations Reveal Structural Differences among Allelic Variants of Membrane-Anchored Cytochrome P450 2D6 | Q57151636 | ||
| CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories | Q57461514 | ||
| Role of Extracellular Loops and Membrane Lipids for Ligand Recognition in the Neuronal Adenosine Receptor Type 2A: An Enhanced Sampling Simulation Study | Q57471905 | ||
| Intriguing role of water in protein-ligand binding studied by neutron crystallography on trypsin complexes | Q58769381 | ||
| Structural Prediction of the Dimeric Form of the Mammalian Translocator Membrane Protein TSPO: A Key Target for Brain Diagnostics | Q58778891 | ||
| P304 | page(s) | 355-365 | |
| P577 | publication date | 2020-02-12 | |
| P1433 | published in | Computational and Structural Biotechnology Journal | Q19865804 |
| P1476 | title | Applications of water molecules for analysis of macromolecule properties | |
| P478 | volume | 18 |
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