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Computational combinatorial ligand design: Application to human ?-thrombin

https://doi.org/10.1007/bf00124471
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Design neuartiger, nichtpeptidischer Thrombin‐Inhibitoren und Struktur eines Thrombin‐Inhibitor‐Komplexes
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Computer Simulation of Molecular Dynamics: Methodology, Applications, and Perspectives in Chemistry
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Optimization of the Biological Activity of Combinatorial Compound Libraries by a Genetic Algorithm
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The refined 1.9 A crystal structure of human alpha‐thrombin: interaction with D‐Phe‐Pro‐Arg chloromethylketone and significance of the Tyr‐Pro‐Pro‐Trp insertion segment.
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CHARMM : A program for macromolecular energy, minimization, and dynamics calculations
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Calculating the electrostatic potential of molecules in solution: Method and error assessment
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Solving the finite difference linearized Poisson‐Boltzmann equation: A comparison of relaxation and conjugate gradient methods
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Calculating electrostatic forces from grid‐calculated potentials
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Dielectric boundary smoothing in finite difference solutions of the poisson equation: An approach to improve accuracy and convergence
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Electrostatic energy calculations by a Finite‐difference method: Rapid calculation of charge–solvent interaction energies
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Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis
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Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison
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Comparative modeling methods: Application to the family of the mammalian serine proteases
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Functionality maps of binding sites: A multiple copy simultaneous search method
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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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Comparative Protein Modelling by Satisfaction of Spatial Restraints
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Structure of a Retro-binding Peptide Inhibitor Complexed with Human α-Thrombin
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Structure-Based Ligand Design
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MAB, a generally applicable molecular force field for structure modelling in medicinal chemistry
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Functionality map analysis of the active site cleft of human thrombin
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Group contributions to the thermodynamic properties of non-ionic organic solutes in dilute aqueous solution
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Crystal structures of HIV-1 protease-inhibitor complexes
inferredcites →https://doi.org/10.1007/bf02171858openalex-snapshot
Crystal structures of thrombin and thrombin complexes as a framework for antithrombotic drug design
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Small-molecule inhibitors of thrombin
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Computational combinatorial chemistry for de novo ligand design: Review and assessment
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Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian dynamics program
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Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program
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The interpretation of protein structures: Estimation of static accessibility
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Calculation of the electric potential in the active site cleft due to α-helix dipoles
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Refined structure of the Hirudin-thrombin complex
inferredcites →https://doi.org/10.1016/0049-3848(79)90014-8openalex-snapshot
D-PHE-PRO-ARGCH2Cl-A selective affinity label for thrombin
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Synthetic low-molecular weight thrombin inhibitors: molecular design and pharmacological profile
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Crystallographic analysis at 3.0-A resolution of the binding to human thrombin of four active site-directed inhibitors.
inferredcites →https://doi.org/10.1017/s0305004100016108openalex-snapshot
Note on Exchange Phenomena in the Thomas Atom
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Kinetic and Crystallographic Studies of Thrombin with Ac-(D)Phe-Pro-boroArg-OH and Its Lysine, Amidine, Homolysine, and Ornithine Analogs
inferredcites →https://doi.org/10.1021/bi00496a010openalex-snapshot
pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model
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Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models
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Absolute pKa calculations with continuum dielectric methods
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Continuum model calculations of solvation free energies: accurate evaluation of electrostatic contributions
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Theory of hydrophobic bonding. II. Correlation of hydrocarbon solubility in water with solvent cavity surface area
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Multiple Highly Diverse Structures Complementary to Enzyme Binding Sites: Results of Extensive Application of a de Novo Design Method Incorporating Combinatorial Growth
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Semianalytical treatment of solvation for molecular mechanics and dynamics
inferredcites →https://doi.org/10.1021/ja00181a020openalex-snapshot
Enhanced sampling in molecular dynamics: use of the time-dependent Hartree approximation for a simulation of carbon monoxide diffusion through myoglobin
inferredcites →https://doi.org/10.1021/jm00034a001openalex-snapshot
Application of the Three-Dimensional Structures of Protein Target Molecules in Structure-Based Drug Design
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Applications of Combinatorial Technologies to Drug Discovery. 1. Background and Peptide Combinatorial Libraries
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Applications of Combinatorial Technologies to Drug Discovery. 2. Combinatorial Organic Synthesis, Library Screening Strategies, and Future Directions
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Design and Synthesis of Potent and Highly Selective Thrombin Inhibitors
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GroupBuild: a fragment-based method for de novo drug design
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Multiple copy simultaneous search and construction of ligands in binding sites: application to inhibitors of HIV-1 aspartic proteinase
inferredcites →https://doi.org/10.1021/jm00113a007openalex-snapshot
Crystallographic and molecular modeling studies on trypanosomal triosephosphate isomerase: a critical assessment of the predicted and observed structures of the complex with 2-phosphoglycerate
inferredcites →https://doi.org/10.1021/jm00114a001openalex-snapshot
NMR studies of molecular complexes as a tool in drug design
inferredcites →https://doi.org/10.1038/248338a0openalex-snapshot
Hydrophobic bonding and accessible surface area in proteins
inferredcites →https://doi.org/10.1038/347631a0openalex-snapshot
Molecular dynamics simulations in biology
inferredcites →https://doi.org/10.1073/pnas.90.17.8048openalex-snapshot
Molecular basis for the inhibition of human alpha-thrombin by the macrocyclic peptide cyclotheonamide A.
inferredcites →https://doi.org/10.1080/00268978400102061openalex-snapshot
Regular representation of irregular charge distributions
inferredcites →https://doi.org/10.1080/08927029308022164openalex-snapshot
Predicting the Structure of the Flavodoxin fromEschericia coliby Homology Modeling, Distance Geometry and Molecular Dynamics
inferredcites →https://doi.org/10.1126/science.2047852openalex-snapshot
Structures of Larger Proteins in Solution: Three- and Four-Dimensional Heteronuclear NMR Spectroscopy
inferredcites →https://doi.org/10.1126/science.257.5073.1078openalex-snapshot
Structure-Based Strategies for Drug Design and Discovery
inferredcites →https://doi.org/10.1126/science.7761829openalex-snapshot
Classical Electrostatics in Biology and Chemistry
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Rational Design of Potent, Bioavailable, Nonpeptide Cyclic Ureas as HIV Protease Inhibitors

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Docking small ligands in flexible binding sites
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Structure-based ligand design by dynamically assembling molecular building blocks at binding site
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Exhaustive docking of molecular fragments with electrostatic solvation
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Locating interaction sites on proteins: The crystal structure of thermolysin soaked in 2% to 100% isopropanol
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The use of affinity adsorbents in expanded bed adsorption
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Efficient electrostatic solvation model for protein-fragment docking
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Solvation energy density occlusion approximation for evaluation of desolvation penalties in biomolecular interactions
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Fragment‐Based Drug Design: Considerations for Good ADME Properties
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Docking and Scoring for Structure‐based Drug Design
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Structure‐based ligand design by a build‐up approach and genetic algorithm search in conformational space
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Receptor-Based Prediction of Binding Affinities
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A recursive algorithm for efficient combinatorial library docking
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Hydrophobicity maps and docking of molecular fragments with solvation
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Growmol, A De novo Computer Program, and its Application to Thermolysin and Pepsin: Results of the Design and Synthesis of a Novel Inhibitor
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Fragment-Based De Novo Design of Cyclin-Dependent Kinase 2 Inhibitors
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The multi-copy simultaneous search methodology: a fundamental tool for structure-based drug design
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Computational identification of epitopes in the glycoproteins of novel bunyavirus (SFTS virus) recognized by a human monoclonal antibody (MAb 4-5)
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Discovery of dual ZAP70 and Syk kinases inhibitors by docking into a rare C-helix-out conformation of Syk
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Identification and mapping of small-molecule binding sites in proteins: computational tools for structure-based drug design
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Chapter 8. Antithrombotics/Serine Proteases
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Computational approaches to structure-based ligand design
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Towards structural models of molecular recognition in olfactory receptors
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Hydrophobicity and functionality maps of farnesyltransferase
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Computational approaches to molecular recognition
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BMaps: A Web Application for Fragment-Based Drug Design and Compound Binding Evaluation
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Disrupting Amyloid Filaments of Tau by Means of Electric Fields
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Predicting Fragment Binding Poses Using a Combined MCSS MM-GBSA Approach
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Combining Solvent Thermodynamic Profiles with Functionality Maps of the Hsp90 Binding Site to Predict the Displacement of Water Molecules
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Fragment-Based de Novo Ligand Design by Multiobjective Evolutionary Optimization
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Use of MCSS to Design Small Targeted Libraries: Application to Picornavirus Ligands
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Structure Activity Relationship by NMR and by Computer: A Comparative Study
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Functionality Maps of the ATP Binding Site of DNA Gyrase B: Generation of a Consensus Model of Ligand Binding
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Automatic and Efficient Decomposition of Two-Dimensional Structures of Small Molecules for Fragment-Based High-Throughput Docking
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Computer-Aided Design of Chiral Ligands. Part 2. Functionality Mapping as a Method To Identify Stereocontrol Elements for Asymmetric Reactions
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Continuum Electrostatic Energies of Macromolecules in Aqueous Solutions
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CombiDOCK: Structure-based combinatorial docking and library design
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Design of dimerization inhibitors of HIV-1 aspartic proteinase: A computer-based combinatorial approach
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A recursive algorithm for efficient combinatorial library docking
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Hydrophobicity maps and docking of molecular fragments with solvation
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Predicting sequences and structures of MHC-binding peptides: a computational combinatorial approach
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Receptor-based prediction of binding affinities
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Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors
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Docking, virtual high throughput screening and in silico fragment‐based drug design
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Design of peptide inhibitors of human papillomavirus 16 (HPV16) transcriptional regulator E1–E2 formation
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Computational identification of antibody epitopes of human papillomavirus 16 (HPV16) L1 proteins
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Computer-Aided Design of Thrombin Inhibitors
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An Evolutionary Approach for Structure-based Design of Natural and Non-natural Peptidic Ligands
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Design of Small Molecule Libraries for NMR Screening and Other Applications in Drug Discovery
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Computational Prediction of the Epitopes of HA1 Protein of Influenza Viruses to its Neutralizing Antibodies
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Computational Identification of Antibody Epitopes on the Dengue Virus NS1 Protein
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Solvents to Fragments to Drugs: MD Applications in Drug Design
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