| scholarly article | Q13442814 |
| P356 | DOI | 10.3390/MOLECULES21111604 |
| P8608 | Fatcat ID | release_cle3mpptnrcchjtddh3p45kt4a |
| P932 | PMC publication ID | 6274120 |
| P698 | PubMed publication ID | 27886114 |
| P2093 | author name string | Shigenori Tanaka | |
| Shota Uehara | |||
| P2860 | cites work | The Protein Data Bank | Q24515306 |
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| Structure of HIV-1 protease in complex with potent inhibitor KNI-272 determined by high-resolution X-ray and neutron crystallography | Q27654045 | ||
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| Replacement of water molecules in a phosphate binding site by furanoside-appended lin-benzoguanine ligands of tRNA-guanine transglycosylase (TGT) | Q27696473 | ||
| Differential Water Thermodynamics Determine PI3K-Beta/Delta Selectivity for Solvent-Exposed Ligand Modifications | Q27704815 | ||
| Substrate specificity and affinity of a protein modulated by bound water molecules | Q27728486 | ||
| Structural comparison of two serine proteinase-protein inhibitor complexes: eglin-c-subtilisin Carlsberg and CI-2-subtilisin Novo | Q27728514 | ||
| Structure of HIV-1 protease with KNI-272, a tight-binding transition-state analog containing allophenylnorstatine | Q27732560 | ||
| Structure-based design of potent inhibitors of scytalone dehydratase: displacement of a water molecule from the active site | Q27766749 | ||
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| Grid inhomogeneous solvation theory: hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril | Q28387381 | ||
| Spatial analysis and quantification of the thermodynamic driving forces in protein-ligand binding: binding site variability | Q28388743 | ||
| Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald | Q40291611 | ||
| Enthalpy-Entropy Compensation upon Molecular Conformational Changes | Q41119903 | ||
| Just add water! The effect of water on the specificity of protein-ligand binding sites and its potential application to drug design | Q41318459 | ||
| Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST. | Q41339143 | ||
| Molecular simulations with solvent competition quantify water displaceability and provide accurate interaction maps of protein binding sites | Q42184980 | ||
| Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking | Q42251037 | ||
| Combining solvent thermodynamic profiles with functionality maps of the Hsp90 binding site to predict the displacement of water molecules | Q42263771 | ||
| WATsite: hydration site prediction program with PyMOL interface | Q42407198 | ||
| A force field with discrete displaceable waters and desolvation entropy for hydrated ligand docking | Q42557837 | ||
| Assessment of programs for ligand binding affinity prediction | Q43105884 | ||
| Structural properties of hydration shell around various conformations of simple polypeptides | Q43128047 | ||
| Rapid context-dependent ligand desolvation in molecular docking | Q43624519 | ||
| Water network perturbation in ligand binding: adenosine A(2A) antagonists as a case study. | Q44760042 | ||
| Investigation on the effect of key water molecules on docking performance in CSARdock exercise | Q45150094 | ||
| Contributions of water transfer energy to protein-ligand association and dissociation barriers: Watermap analysis of a series of p38α MAP kinase inhibitors | Q46377411 | ||
| Binding mode prediction of cytochrome p450 and thymidine kinase protein-ligand complexes by consideration of water and rescoring in automated docking. | Q46414034 | ||
| Extracting hydration sites around proteins from explicit water simulations | Q46636331 | ||
| A discussion of measures of enrichment in virtual screening: comparing the information content of descriptors with increasing levels of sophistication | Q46717923 | ||
| Modeling water molecules in protein-ligand docking using GOLD. | Q46725683 | ||
| Thermodynamics of buried water clusters at a protein-ligand binding interface | Q46938920 | ||
| Consideration of molecular weight during compound selection in virtual target-based database screening | Q47173464 | ||
| High-performance drug discovery: computational screening by combining docking and molecular dynamics simulations | Q28476233 | ||
| Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes | Q29397708 | ||
| AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility | Q29547658 | ||
| A semiempirical free energy force field with charge-based desolvation | Q29614316 | ||
| Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation | Q29616387 | ||
| Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes | Q29616736 | ||
| Locating missing water molecules in protein cavities by the three-dimensional reference interaction site model theory of molecular solvation. | Q30358933 | ||
| Incorporating replacement free energy of binding-site waters in molecular docking. | Q30359220 | ||
| Evaluating Free Energies of Binding and Conservation of Crystallographic Waters Using SZMAP. | Q30376731 | ||
| A computational procedure for determining energetically favorable binding sites on biologically important macromolecules | Q30406755 | ||
| Prediction of the water content in protein binding sites | Q30495095 | ||
| PDB-wide collection of binding data: current status of the PDBbind database | Q30858984 | ||
| PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data | Q31026348 | ||
| Impact of Surface Water Layers on Protein--Ligand Binding: How Well Are Experimental Data Reproduced by Molecular Dynamics Simulations in a Thermolysin Test Case? | Q31033244 | ||
| Mass spectrometric and thermodynamic studies reveal the role of water molecules in complexes formed between SH2 domains and tyrosyl phosphopeptides | Q32014468 | ||
| Investigation of MM-PBSA rescoring of docking poses | Q33332674 | ||
| Exploiting ordered waters in molecular docking | Q33357656 | ||
| Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa. | Q33874099 | ||
| Nicotinic pharmacophore: the pyridine N of nicotine and carbonyl of acetylcholine hydrogen bond across a subunit interface to a backbone NH. | Q34067895 | ||
| AutoDock4(Zn): an improved AutoDock force field for small-molecule docking to zinc metalloproteins | Q34089389 | ||
| Perspectives on factor Xa inhibition | Q34137471 | ||
| Water structure, dynamics, and spectral signatures: changes upon model cavity-ligand recognition | Q34308445 | ||
| Docking and scoring in virtual screening for drug discovery: methods and applications | Q34364227 | ||
| Further development and validation of empirical scoring functions for structure-based binding affinity prediction | Q34526566 | ||
| Automated docking of substrates to proteins by simulated annealing | Q34640538 | ||
| Role of the active-site solvent in the thermodynamics of factor Xa ligand binding | Q34748976 | ||
| Molecular docking: a powerful approach for structure-based drug discovery | Q35150471 | ||
| Inclusion of solvation and entropy in the knowledge-based scoring function for protein-ligand interactions | Q35419556 | ||
| Molecular binding: Under water's influence | Q36277660 | ||
| Energetics of displacing water molecules from protein binding sites: consequences for ligand optimization | Q37439036 | ||
| The discovery and development of rivaroxaban, an oral, direct factor Xa inhibitor | Q37821752 | ||
| Challenges and advances in computational docking: 2009 in review | Q37848281 | ||
| New hypotheses about the structure-function of proprotein convertase subtilisin/kexin type 9: analysis of the epidermal growth factor-like repeat A docking site using WaterMap | Q39686913 | ||
| Enthalpy-entropy compensation phenomena in water solutions of proteins and small molecules: A ubiquitous properly of water | Q39992903 | ||
| Dewetting transitions in protein cavities | Q40270287 | ||
| Protein-ligand docking using fitness learning-based artificial bee colony with proximity stimuli. | Q50583550 | ||
| SODOCK: swarm optimization for highly flexible protein-ligand docking. | Q51091845 | ||
| Application of a post-docking procedure based on MM-PBSA and MM-GBSA on single and multiple protein conformations. | Q51299884 | ||
| Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database. | Q51664708 | ||
| Classification of water molecules in protein binding sites. | Q51922692 | ||
| SuperStar: a knowledge-based approach for identifying interaction sites in proteins. | Q52211818 | ||
| Ligand solvation in molecular docking. | Q52214239 | ||
| Electrostatic effects in proteins: comparison of dielectric and charge models | Q52422371 | ||
| Analysis of water patterns in protein kinase binding sites. | Q54591150 | ||
| Adding calorimetric data to decision making in lead discovery: a hot tip | Q56452754 | ||
| Biomolecular energy calculations using transputer technology | Q69749209 | ||
| Hydration in drug design. 1. Multiple hydrogen-bonding features of water molecules in mediating protein-ligand interactions | Q71491557 | ||
| Thermodynamic contributions of the ordered water molecule in HIV-1 protease | Q73442110 | ||
| Virtual screening workflow development guided by the "receiver operating characteristic" curve approach. Application to high-throughput docking on metabotropic glutamate receptor subtype 4 | Q81598760 | ||
| Computing the thermodynamic contributions of interfacial water | Q83065308 | ||
| WScore: A Flexible and Accurate Treatment of Explicit Water Molecules in Ligand-Receptor Docking | Q89138839 | ||
| P275 | copyright license | Creative Commons Attribution 4.0 International | Q20007257 |
| P6216 | copyright status | copyrighted | Q50423863 |
| P433 | issue | 11 | |
| P407 | language of work or name | English | Q1860 |
| P921 | main subject | thermodynamics | Q11473 |
| P577 | publication date | 2016-11-23 | |
| P1433 | published in | Molecules | Q151332 |
| P1476 | title | AutoDock-GIST: Incorporating Thermodynamics of Active-Site Water into Scoring Function for Accurate Protein-Ligand Docking | |
| P478 | volume | 21 |
| Q89984751 | Applications of water molecules for analysis of macromolecule properties |
| Q47348724 | GPCRs: What Can We Learn from Molecular Dynamics Simulations? |
| Q90367172 | Hydration of Aromatic Heterocycles as an Adversary of π-Stacking |
| Q92372738 | Pharmacophoric Site Identification and Inhibitor Design for Autotaxin |
| Q90559248 | Solvation Free Energy as a Measure of Hydrophobicity: Application to Serine Protease Binding Interfaces |
| Q60960514 | Solvents to Fragments to Drugs: MD Applications in Drug Design |
| Q41476961 | Testing inhomogeneous solvation theory in structure-based ligand discovery |
| Q88567611 | Thermodynamic Insight into the Effects of Water Displacement and Rearrangement upon Ligand Modifications using Molecular Dynamics Simulations |
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