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Three-dimensional hydrogen-bond geometry and probability information from a crystal survey
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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HOOK: A program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding site
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The Use of Composite Crystal-field Environments in Molecular Recognition and the de Novo Design of Protein Ligands
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Satisfying Hydrogen Bonding Potential in Proteins
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Hydrogen Bonding in Biological Structures
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Molecular surface-volume and property matching to superpose flexible dissimilar molecules
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The computer program LUDI: A new method for the de novo design of enzyme inhibitors
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LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads
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Automatic superposition of drug molecules based on their common receptor site
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A fast new approach to pharmacophore mapping and its application to dopaminergic and benzodiazepine agonists
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Geometries of functional group interactions in enzyme-ligand complexes: Guides for receptor modelling
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Hydrogen bonding in biological structures
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A survey of O-H⋯O hydrogen bond geometries determined by neutron diffraction
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The protein data bank: A computer-based archival file for macromolecular structures
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The C-H.cntdot..cntdot..cntdot.O hydrogen bond in crystals: what is it?
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The development of versions 3 and 4 of the Cambridge Structural Database System
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Hydrogen bonds as design elements in organic chemistry
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Hydrogen bonds to carboxylate groups. Syn/anti distributions and steric effects
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Stereochemistry of phosphate-Lewis acid interactions: implications for nucleic acid structure and recognition
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Hydrogen-bond formation in nitroanilines: the first step in designing acentric materials
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Lone-pair directionality in hydrogen-bond potential functions for molecular mechanics calculations: the inhibition of human carbonic anhydrase II by sulfonamides
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Geometry of the nitrogen-hydrogen...oxygen-carbon (N-H...O:C) hydrogen bond. 2. Three-center (bifurcated) and four-center (trifurcated) bonds
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Directional hydrogen bonding to sp2- and sp3-hybridized oxygen atoms and its relevance to ligand-macromolecule interactions
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Intermolecular interactions of the carbon-fluorine bond: the crystallographic environment of fluorinated carboxylic acids and related structures
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Geometry of the imino-carbonyl (N-H...O:C) hydrogen bond. 1. Lone-pair directionality
inferredcites →https://doi.org/10.1021/ja00383a012openalex-snapshot
Crystallographic evidence for the existence of CH.cntdot..cntdot..cntdot.O, CH.cntdot..cntdot..cntdot.N and CH.cntdot..cntdot..cntdot.Cl hydrogen bonds
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Directional preferences of nonbonded atomic contacts with divalent sulfur. 1. Electrophiles and nucleophiles
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New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure
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A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
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Scales of solute hydrogen-bonding: their construction and application to physicochemical and biochemical processes
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Hydrogen bonding. Part 9. Solute proton donor and proton acceptor scales for use in drug design
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Hydrogen bonds to carboxylate groups. The question of three-centre interactions
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Model solvent systems for QSAR. Part 3. An LSER analysis of the ‘critical quartet.’ New light on hydrogen bond strength and directionality
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Ab initio models for receptor–ligand interactions in proteins. Part 1. Models for asparagine, glutamine, serine, threonine and tyrosine
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Automated site-directed drug design: a general algorithm for knowledge acquisition about hydrogen-bonding regions at protein surfaces
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Automated site-directed drug design : the prediction and observation of ligand point positions at hydrogen-bonding regions on protein surfaces
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3D structure determination from electron-microscope images: electron crystallography of staurolite
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Comparison of X-ray and neutron diffraction results for the N-H ...O=C hydrogen bond
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The geometry of the N–H...O=C hydrogen bond. 3. Hydrogen-bond distances and angles
inferredcites →https://doi.org/10.1107/s0108768189003666openalex-snapshot
Hydrogen-bond distances and angles in the structures of amino acids and peptides
inferredcites →https://doi.org/10.1107/s0108768192003021openalex-snapshot
Nature of the hydrogen bond: crystallographic versus theoretical description of the O-H ... N( sp 2 ) hydrogen bond
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A database study of intermolecular NH...O hydrogen bonds for carboxylates, sulfonates and monohydrogen phosphonates
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inferred← citeshttps://doi.org/10.1021/bi4003327openalex-snapshot
Complex Structures between the N-Type Calcium Channel (CaV2.2) and ω-Conotoxin GVIA Predicted via Molecular Dynamics
inferred← citeshttps://doi.org/10.1021/bm4004496openalex-snapshot
Effect of 3D Matrix Compositions on the Efficacy of EGFR Inhibition in Pancreatic Ductal Adenocarcinoma Cells
inferred← citeshttps://doi.org/10.1021/cb200413aopenalex-snapshot
Chemical Correction of Pre-mRNA Splicing Defects Associated with Sequestration of Muscleblind-like 1 Protein by Expanded r(CAG)-Containing Transcripts
inferred← citeshttps://doi.org/10.1021/cb300135hopenalex-snapshot
A Small Molecule That Targets r(CGG)exp and Improves Defects in Fragile X-Associated Tremor Ataxia Syndrome
inferred← citeshttps://doi.org/10.1021/cg3014656openalex-snapshot
Relationship between Stereochemistry and Charge Density in Hydrogen Bonds with Oxygen Acceptors
inferred← citeshttps://doi.org/10.1021/cg8002788openalex-snapshot
Statistics-Based Design of Multicomponent Molecular Crystals with the Three-Center Hydrogen Bond
inferred← citeshttps://doi.org/10.1021/ci100194kopenalex-snapshot
GAPE: An Improved Genetic Algorithm for Pharmacophore Elucidation
inferred← citeshttps://doi.org/10.1021/ci100250zopenalex-snapshot
Toward the Discovery of Functional Transthyretin Amyloid Inhibitors: Application of Virtual Screening Methods
inferred← citeshttps://doi.org/10.1021/ci200237copenalex-snapshot
Minor Groove Binders and Drugs Targeting Proteins Cover Complementary Regions in Chemical Shape Space
inferred← citeshttps://doi.org/10.1021/ci300096copenalex-snapshot
Identification of Novel Liver X Receptor Activators by Structure-Based Modeling
inferred← citeshttps://doi.org/10.1021/ci800386vopenalex-snapshot
Hybrid Structure-Based Virtual Screening Protocol for the Identification of Novel BACE1 Inhibitors
inferred← citeshttps://doi.org/10.1021/ci900309sopenalex-snapshot
Combinatorial Library Enumeration and Lead Hopping using Comparative Interaction Fingerprint Analysis and Classical 2D QSAR Methods for Seeking Novel GABAA α3 Modulators
inferred← citeshttps://doi.org/10.1021/ci900498nopenalex-snapshot
HPPD: Ligand- and Target-Based Virtual Screening on a Herbicide Target
inferred← citeshttps://doi.org/10.1021/ct800267xopenalex-snapshot
Geometrical Preferences of the Hydrogen Bonds on Protein−Ligand Binding Interface Derived from Statistical Surveys and Quantum Mechanics Calculations
inferred← citeshttps://doi.org/10.1021/ja2011115openalex-snapshot
Restructuring the Crystalline Cellulose Hydrogen Bond Network Enhances Its Depolymerization Rate
inferred← citeshttps://doi.org/10.1021/ja210088vopenalex-snapshot
Design of a Bioactive Small Molecule That Targets the Myotonic Dystrophy Type 1 RNA via an RNA Motif–Ligand Database and Chemical Similarity Searching
inferred← citeshttps://doi.org/10.1021/jacs.6b06566openalex-snapshot
Hydrogen Bonding of 1,2-Azaborines in the Binding Cavity of T4 Lysozyme Mutants: Structures and Thermodynamics
inferred← citeshttps://doi.org/10.1021/jacsau.4c00213openalex-snapshot
Gauging Iron–Sulfur Cubane Reactivity from Covalency: Trends with Oxidation State
inferred← citeshttps://doi.org/10.1021/jacsau.5c00447openalex-snapshot
WatCon: A Python Tool for Analysis of Conserved Water Networks Across Protein Families
inferred← citeshttps://doi.org/10.1021/jm011039xopenalex-snapshot
Development of New Hydrogen-Bond Descriptors and Their Application to Comparative Molecular Field Analyses
inferred← citeshttps://doi.org/10.1021/jm034222uopenalex-snapshot
Scaffold Hopping in De Novo Design. Ligand Generation in the Absence of Receptor Information
inferred← citeshttps://doi.org/10.1021/jm0603365openalex-snapshot
Comparison of Shape-Matching and Docking as Virtual Screening Tools
inferred← citeshttps://doi.org/10.1021/jm300265jopenalex-snapshot
Structure-Based Design, Synthesis, and Characterization of Dual Hotspot Small-Molecule HIV-1 Entry Inhibitors
inferred← citeshttps://doi.org/10.1021/jm501345yopenalex-snapshot
New Compstatin Peptides Containing N-Terminal Extensions and Non-Natural Amino Acids Exhibit Potent Complement Inhibition and Improved Solubility Characteristics
inferred← citeshttps://doi.org/10.1021/jm9806998openalex-snapshot
New 4-Point Pharmacophore Method for Molecular Similarity and Diversity Applications: Overview of the Method and Applications, Including a Novel Approach to the Design of Combinatorial Libraries Containing Privileged Substructures
inferred← citeshttps://doi.org/10.1021/jp104865wopenalex-snapshot
Accurate Predictions of Water Cluster Formation, (H2O)n=2−10
inferred← citeshttps://doi.org/10.1021/jp2048844openalex-snapshot
Probing the Early Events Associated with Liquid Ammonia Pretreatment of Native Crystalline Cellulose
inferred← citeshttps://doi.org/10.1021/jp401159ropenalex-snapshot
Determining In Situ Protein Conformation and Orientation from the Amide-I Sum-Frequency Generation Spectrum: Theory and Experiment
inferred← citeshttps://doi.org/10.1021/jp810772aopenalex-snapshot
Hydrogen Bonds in Membrane Proteins
inferred← citeshttps://doi.org/10.1023/a:1007900527102openalex-snapshot
An automated method for predicting the positions of hydrogen-bonding atoms in binding sites
inferred← citeshttps://doi.org/10.1023/a:1007923124523openalex-snapshot
The orientation of N-H...O=C and N-H...N hydrogen bonds in biological systems: How good is a point charge as a model for a hydrogen bonding atom?
inferred← citeshttps://doi.org/10.1023/a:1007934413448openalex-snapshot
IsoStar: A library of information about nonbonded interactions
inferred← citeshttps://doi.org/10.1023/a:1008109717641openalex-snapshot
Simple knowledge-based descriptors to predict protein-ligand interactions. Methodology and validation
inferred← citeshttps://doi.org/10.1023/a:1011102129244openalex-snapshot
slate: A method for the superposition of flexible ligands
inferred← citeshttps://doi.org/10.1023/a:1016361910530openalex-snapshot
3D hydrogen bond thermodynamics (HYBOT) potentials in molecular modelling
inferred← citeshttps://doi.org/10.1023/a:1017037831628openalex-snapshot
3D QSAR: current state, scope, and limitations
inferred← citeshttps://doi.org/10.1023/a:1027224402069openalex-snapshot
Progress in force-field calculations of molecular interaction fields and intermolecular interactions
inferred← citeshttps://doi.org/10.1023/a:1027268223451openalex-snapshot
Molecular dynamics simulations: a tool for drug design
inferred← citeshttps://doi.org/10.1023/a:1027346709963openalex-snapshot
A new method for estimating the importance of hydrogen-bonding groups in the binding site of a protein
inferred← citeshttps://doi.org/10.1023/b:jcam.0000030032.81753.b4openalex-snapshot
The effect of tightly bound water molecules on the structural interpretation of ligand-derived pharmacophore models
inferred← citeshttps://doi.org/10.1038/nrd2615openalex-snapshot
Pseudoreceptor models in drug design: bridging ligand- and receptor-based virtual screening
inferred← citeshttps://doi.org/10.1038/pj.2015.82openalex-snapshot
Molecular dynamics simulation of telomeric single-stranded DNA and POT1
inferred← citeshttps://doi.org/10.1038/s41429-021-00412-7openalex-snapshot
Identification of a bacteria-produced benzisoxazole with antibiotic activity against multi-drug resistant Acinetobacter baumannii
inferred← citeshttps://doi.org/10.1038/s41467-019-09691-zopenalex-snapshot
Discovery of processive catalysis by an exo-hydrolase with a pocket-shaped active site
inferred← citeshttps://doi.org/10.1038/s41467-022-30506-1openalex-snapshot
Cryo-EM structures define ubiquinone-10 binding to mitochondrial complex I and conformational transitions accompanying Q-site occupancy
inferred← citeshttps://doi.org/10.1038/s41594-021-00637-yopenalex-snapshot
Structural basis of RNA processing by human mitochondrial RNase P
inferred← citeshttps://doi.org/10.1038/s41598-019-53410-zopenalex-snapshot
Discovery of a potent small molecule inhibiting Huntington’s disease (HD) pathogenesis via targeting CAG repeats RNA and Poly Q protein
inferred← citeshttps://doi.org/10.1038/s41598-020-78782-5openalex-snapshot
Acetylcholinesterase and butyrylcholinesterase inhibitory activities of khellactone coumarin derivatives isolated from Peucedanum japonicum Thurnberg
inferred← citeshttps://doi.org/10.1038/s41598-021-01529-3openalex-snapshot
Piperine analogs arrest c-myc gene leading to downregulation of transcription for targeting cancer
inferred← citeshttps://doi.org/10.1038/s41598-021-93458-4openalex-snapshot
Acetylcholinesterase and monoamine oxidase-B inhibitory activities by ellagic acid derivatives isolated from Castanopsis cuspidata var. sieboldii
inferred← citeshttps://doi.org/10.1039/b002357oopenalex-snapshot
Empirical and molecular modeling study of the pyridinium species RHPP+, an abundant and potentially neurotoxic metabolite of haloperidol
inferred← citeshttps://doi.org/10.1039/c4mb00239copenalex-snapshot
Validation of a computational docking methodology to identify the non-covalent binding site of ligands to DNA
inferred← citeshttps://doi.org/10.1039/c8cp05470copenalex-snapshot
Competitor analysis of functional group H-bond donor and acceptor properties using the Cambridge Structural Database
inferred← citeshttps://doi.org/10.1039/c9cp02338kopenalex-snapshot
Molecular mechanisms of 33-mer gliadin peptide oligomerisation
inferred← citeshttps://doi.org/10.1039/c9ob01008dopenalex-snapshot
Exploring the strength of a hydrogen bond as a function of steric environment using 1,2-azaborine ligands and engineered T4 lysozyme receptors
inferred← citeshttps://doi.org/10.1039/d3sc04653bopenalex-snapshot
Sample efficient reinforcement learning with active learning for molecular design
inferred← citeshttps://doi.org/10.1039/d5sc09263aopenalex-snapshot
Synthesizability via reward engineering: expanding generative molecular design into synthetic space
inferred← citeshttps://doi.org/10.1042/bcj20160737openalex-snapshot
Modulation of prion polymerization and toxicity by rationally designed peptidomimetics
inferred← citeshttps://doi.org/10.1055/s-0032-1328129openalex-snapshot
Characterisation of Nox4 Inhibitors from Edible Plants
inferred← citeshttps://doi.org/10.1073/pnas.2004445117openalex-snapshot
Atomistic structure and dynamics of the human MHC-I peptide-loading complex
inferred← citeshttps://doi.org/10.1073/pnas.2020486118openalex-snapshot
Early-stage dynamics of chloride ion–pumping rhodopsin revealed by a femtosecond X-ray laser
inferred← citeshttps://doi.org/10.1074/jbc.m114.589200openalex-snapshot
Discovery of Mycobacterium tuberculosis α-1,4-Glucan Branching Enzyme (GlgB) Inhibitors by Structure- and Ligand-based Virtual Screening
inferred← citeshttps://doi.org/10.1074/jbc.m117.788299openalex-snapshot
Arjunolic acid, a peroxisome proliferator-activated receptor α agonist, regresses cardiac fibrosis by inhibiting non-canonical TGF-β signaling
inferred← citeshttps://doi.org/10.1080/00268976.2013.826392openalex-snapshot
Force field-based conformational searches: efficiency and performance for peptide receptor complexes
inferred← citeshttps://doi.org/10.1080/07391102.2013.872052openalex-snapshot
3D-QSAR studies and shape based virtual screening for identification of novel hits to inhibit MbtA inMycobacterium tuberculosis
inferred← citeshttps://doi.org/10.1080/07391102.2018.1491418openalex-snapshot
Identification of protegrin-1 as a stable and nontoxic scaffold among protegrin family – a computational approach
inferred← citeshttps://doi.org/10.1080/07391102.2020.1763839openalex-snapshot
Discovery of new potential CDK2/VEGFR2 type II inhibitors by fragmentation and virtual screening of natural products
inferred← citeshttps://doi.org/10.1080/07391102.2026.2708778openalex-snapshot
Structural and molecular basis of O-GlcNAcylation-phosphorylation crosstalk in protein Kinase-B (Akt2)
inferred← citeshttps://doi.org/10.1093/hmg/ddq182openalex-snapshot
TUBA1A mutations cause wide spectrum lissencephaly (smooth brain) and suggest that multiple neuronal migration pathways converge on alpha tubulins
inferred← citeshttps://doi.org/10.1093/nar/gkh785openalex-snapshot
A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys
inferred← citeshttps://doi.org/10.1093/nar/gks067openalex-snapshot
Double threading through DNA: NMR structural study of a bis-naphthalene macrocycle bound to a thymine–thymine mismatch
inferred← citeshttps://doi.org/10.1093/nar/gkv1124openalex-snapshot
Nucleotide binding database NBDB – a collection of sequence motifs with specific protein-ligand interactions
inferred← citeshttps://doi.org/10.1093/nargab/lqac101openalex-snapshot
Alignment of major-groove hydrogen bond arrays uncovers shared information between different DNA sequences that bind the same protein
inferred← citeshttps://doi.org/10.1096/fj.201700043ropenalex-snapshot
Modeled structural basis for the recognition of α2–3‐sialyllactose by soluble Klotho
inferred← citeshttps://doi.org/10.1096/fj.201900321ropenalex-snapshot
Soluble klotho regulates TRPC6 calcium signaling via lipid rafts, independent of the FGFR‐FGF23 pathway
inferred← citeshttps://doi.org/10.1101/056531openalex-snapshot
The Wnt segment polarity pathway and TMED2 protein may interact via a lectin- and decoy-type mechanism
inferred← citeshttps://doi.org/10.1101/092460openalex-snapshot
VIP36 preferentially binds to core-fucosylated N-glycans: a molecular docking study
inferred← citeshttps://doi.org/10.1101/2023.07.06.548038openalex-snapshot
Cooperative conformational transitions and the temperature dependence of enzyme catalysis
inferred← citeshttps://doi.org/10.1101/2023.08.23.554490openalex-snapshot
Allosteric activation of the co-receptor BAK1 by the EFR receptor kinase initiates immune signaling
inferred← citeshttps://doi.org/10.1101/2024.01.22.576714openalex-snapshot
Comprehensive epitope mutational scan database enables accurate T cell receptor cross-reactivity prediction
inferred← citeshttps://doi.org/10.1101/2024.12.02.626379openalex-snapshot
The VGCC auxiliary subunit α2δ1 is an extracellular GluA1 interactor and regulates LTP, spatial memory, and seizure susceptibility
inferred← citeshttps://doi.org/10.1107/s090744490200358xopenalex-snapshot
Life-science applications of the Cambridge Structural Database
inferred← citeshttps://doi.org/10.1107/s139900471400724xopenalex-snapshot
Structures of inactive CRP species reveal the atomic details of the allosteric transition that discriminates cyclic nucleotide second messengers
inferred← citeshttps://doi.org/10.1107/s205698902000972xopenalex-snapshot
DL -Piperidinium-2-carboxylate bis(hydrogen peroxide): unusual hydrogen-bonded peroxide chains
inferred← citeshttps://doi.org/10.1109/icip.2006.312766openalex-snapshot
Virtual Craniofacial Reconstruction from Computed Tomography Image Sequences Exhibiting Multiple Fractures
inferred← citeshttps://doi.org/10.1111/j.1747-0285.2011.01262.xopenalex-snapshot
Identification of Novel Inhibitors of Dipeptidylcarboxypeptidase of Leishmania donovani via Ligand‐Based Virtual Screening and Biological Evaluation
inferred← citeshttps://doi.org/10.1126/sciadv.aaz2309openalex-snapshot
Computer simulations explain mutation-induced effects on the DNA editing by adenine base editors
inferred← citeshttps://doi.org/10.1128/mbio.00166-12openalex-snapshot
Emergence of Fatal Avian Influenza in New England Harbor Seals
inferred← citeshttps://doi.org/10.1139/cjc-2019-0421openalex-snapshot
Assessing the feasibility and stability of uracil base flipping in RNA–small molecule complexes using molecular dynamics simulations
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