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Molecular Modelling
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Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94
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BLEEP?potential of mean force describing protein-ligand interactions: I. Generating potential
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BLEEP?potential of mean force describing protein-ligand interactions: II. Calculation of binding energies and comparison with experimental data
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All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data
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Flexible protein–ligand docking by global energy optimization in internal coordinates
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Exhaustive docking of molecular fragments with electrostatic solvation
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The art and practice of structure-based drug design: A molecular modeling perspective
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“Scaffold-Hopping” by Topological Pharmacophore Search: A Contribution to Virtual Screening
inferredcites →https://doi.org/10.1002/1097-0134(20000901)40:4<623::aid-prot70>3.0.co;2-iopenalex-snapshot
Similarity-driven flexible ligand docking
inferredcites →https://doi.org/10.1002/1097-0134(20010501)43:2<217::aid-prot1032>3.0.co;2-gopenalex-snapshot
Ligand-protein inverse docking and its potential use in the computer search of protein targets of a small molecule
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Application and Limitations of X‐ray Crystallographic Data in Structure‐Based Ligand and Drug Design
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Application of statistical potentials to protein structure refinement from low resolution ab initio models
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Classifying “Kinase Inhibitor‐Likeness” by Using Machine‐Learning Methods
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New Inhibitors of the Tat–TAR RNA Interaction Found with a “Fuzzy” Pharmacophore Model
inferredcites →https://doi.org/10.1002/jcc.20090openalex-snapshot
A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force‐field parameter sets 53A5 and 53A6
inferredcites →https://doi.org/10.1002/jcc.20141openalex-snapshot
Evaluation of library ranking efficacy in virtual screening
inferredcites →https://doi.org/10.1002/med.10041openalex-snapshot
Selection criteria for drug‐like compounds
inferredcites →https://doi.org/10.1002/med.10044openalex-snapshot
VLA‐4 antagonists: Potent inhibitors of lymphocyte migration
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Recent advances inde novodesign strategy for practical lead identification
inferredcites →https://doi.org/10.1002/prot.10028openalex-snapshot
Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock
inferredcites →https://doi.org/10.1002/prot.10085openalex-snapshot
Dissecting protein–protein recognition sites
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Recovering the true targets of specific ligands by virtual screening of the protein data bank
inferredcites →https://doi.org/10.1002/prot.20088openalex-snapshot
A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
inferredcites →https://doi.org/10.1002/prot.20149openalex-snapshot
Comparative evaluation of eight docking tools for docking and virtual screening accuracy
inferredcites →https://doi.org/10.1002/prot.20285openalex-snapshot
Optimal docking area: A new method for predicting protein–protein interaction sites
inferredcites →https://doi.org/10.1002/prot.20512openalex-snapshot
Binding MOAD (Mother Of All Databases)
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Evaluation of comparative protein modeling by M ODELLER
inferredcites →https://doi.org/10.1002/qua.10778openalex-snapshot
Semiempirical calculations of binding enthalpy for protein–ligand complexes
inferredcites →https://doi.org/10.1006/jmbi.1996.0776openalex-snapshot
Molecular docking to ensembles of protein structures 1 1Edited by B. Honig
inferredcites →https://doi.org/10.1006/jmbi.1999.3371openalex-snapshot
Knowledge-based scoring function to predict protein-ligand interactions
inferredcites →https://doi.org/10.1006/jmbi.2001.4551openalex-snapshot
FlexE: efficient molecular docking considering protein structure variations
inferredcites →https://doi.org/10.1007/bf00119865openalex-snapshot
FLOG: A system to select ?quasi-flexible? ligands complementary to a receptor of known three-dimensional structure
inferredcites →https://doi.org/10.1007/bf00124387openalex-snapshot
The computer program LUDI: A new method for the de novo design of enzyme inhibitors
inferredcites →https://doi.org/10.1007/bf00124464openalex-snapshot
Placement of medium-sized molecular fragments into active sites of proteins
inferredcites →https://doi.org/10.1007/bf00126743openalex-snapshot
The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
inferredcites →https://doi.org/10.1007/s00214-004-0589-9openalex-snapshot
Application of semiempirical quantum chemical methods as a scoring function in docking
inferredcites →https://doi.org/10.1007/s00894-002-0112-yopenalex-snapshot
Binding site characteristics in structure-based virtual screening: evaluation of current docking tools
inferredcites →https://doi.org/10.1016/0022-2836(82)90153-xopenalex-snapshot
A geometric approach to macromolecule-ligand interactions
inferredcites →https://doi.org/10.1016/0040-4020(80)80168-2openalex-snapshot
Iterative partial equalization of orbital electronegativity—a rapid access to atomic charges
inferredcites →https://doi.org/10.1016/0968-0896(95)00031-bopenalex-snapshot
Conformational changes of small molecules binding to proteins
inferredcites →https://doi.org/10.1016/1074-5521(95)90050-0openalex-snapshot
Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming
inferredcites →https://doi.org/10.1016/j.bbapap.2003.11.028openalex-snapshot
Kinomics—structural biology and chemogenomics of kinase inhibitors and targets
inferredcites →https://doi.org/10.1016/j.bmcl.2004.03.058openalex-snapshot
Hit-to-lead studies: the discovery of potent, orally active, thiophenecarboxamide IKK-2 inhibitors
inferredcites →https://doi.org/10.1016/j.cbpa.2004.05.001openalex-snapshot
High-throughput docking as a source of novel drug leads
inferredcites →https://doi.org/10.1016/j.cbpa.2004.06.002openalex-snapshot
Target-biased scoring approaches and expert systems in structure-based virtual screening
inferredcites →https://doi.org/10.1016/j.cbpa.2004.06.005openalex-snapshot
Predictive ADMET studies, the challenges and the opportunities
inferredcites →https://doi.org/10.1016/j.cbpa.2004.06.008openalex-snapshot
Integrating virtual screening in lead discovery
inferredcites →https://doi.org/10.1016/j.coph.2004.04.007openalex-snapshot
High-throughput X-ray crystallography for drug discovery
inferredcites →https://doi.org/10.1016/j.jmb.2004.01.003openalex-snapshot
Protein Flexibility in Ligand Docking and Virtual Screening to Protein Kinases
inferredcites →https://doi.org/10.1016/j.jmb.2004.02.015openalex-snapshot
Testing a Flexible-receptor Docking Algorithm in a Model Binding Site
inferredcites →https://doi.org/10.1016/j.pbiomolbio.2004.07.011openalex-snapshot
Life in the fast lane for protein crystallization and X-ray crystallography
inferredcites →https://doi.org/10.1016/j.sbi.2004.09.003openalex-snapshot
Automation of NMR structure determination of proteins
inferredcites →https://doi.org/10.1016/j.str.2004.02.031openalex-snapshot
Heterogeneity and Inaccuracy in Protein Structures Solved by X-Ray Crystallography
inferredcites →https://doi.org/10.1016/j.tibtech.2004.12.006openalex-snapshot
Structural genomics of GPCRs
inferredcites →https://doi.org/10.1016/s0006-3495(03)74997-2openalex-snapshot
Development of Unified Statistical Potentials Describing Protein-Protein Interactions
inferredcites →https://doi.org/10.1016/s0022-2836(02)00971-3openalex-snapshot
Sequence Variations within Protein Families are Linearly Related to Structural Variations
inferredcites →https://doi.org/10.1016/s0022-2836(95)80037-9openalex-snapshot
Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation
inferredcites →https://doi.org/10.1016/s0065-3233(03)66009-2openalex-snapshot
All-Atom Simulations Of Protein Folding And Unfolding
inferredcites →https://doi.org/10.1016/s0079-6107(97)00005-9openalex-snapshot
Computational tools for structure-based ligand design
inferredcites →https://doi.org/10.1016/s0167-4838(00)00262-4openalex-snapshot
Inhibitors of dihydrodipicolinate reductase, a key enzyme of the diaminopimelate pathway of Mycobacterium tuberculosis
inferredcites →https://doi.org/10.1016/s0169-409x(96)00423-1openalex-snapshot
Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings
inferredcites →https://doi.org/10.1016/s0969-2126(03)00186-2openalex-snapshot
Pound-Wise but Penny-Foolish
inferredcites →https://doi.org/10.1016/s1047-8477(03)00041-8openalex-snapshot
The protein as a variable in protein crystallization
inferredcites →https://doi.org/10.1016/s1047-8477(03)00046-7openalex-snapshot
High-throughput protein crystallization
inferredcites →https://doi.org/10.1016/s1056-8719(00)00107-6openalex-snapshot
Drug-like properties and the causes of poor solubility and poor permeability
inferredcites →https://doi.org/10.1016/s1093-3263(02)00164-xopenalex-snapshot
LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites
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LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins
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The in silico world of virtual libraries
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Chemical substructures in drug discovery
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Ligand efficiency: a useful metric for lead selection
inferredcites →https://doi.org/10.1016/s1359-6446(05)03477-xopenalex-snapshot
Kinomics: characterizing the therapeutically validated kinase space
inferredcites →https://doi.org/10.1016/s1359-6446(97)01083-0openalex-snapshot
Reactive compounds and in vitro false positives in HTS
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Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models
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Molecular Quantum Similarity and the Fundamentals of QSAR
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Is There a Difference between Leads and Drugs? A Historical Perspective
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Mining High-Throughput Screening Data of Combinatorial Libraries: Development of a Filter to Distinguish Hits from Nonhits
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Assessment of Docking Poses: Interactions-Based Accuracy Classification (IBAC) versus Crystal Structure Deviations
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Strategic Pooling of Compounds for High-Throughput Screening
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Free energy calculations: Applications to chemical and biochemical phenomena
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Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics
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Theoretical Methods for the Description of the Solvent Effect in Biomolecular Systems
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A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
inferredcites →https://doi.org/10.1021/ja00172a038openalex-snapshot
Semianalytical treatment of solvation for molecular mechanics and dynamics
inferredcites →https://doi.org/10.1021/ja003834qopenalex-snapshot
Use of MM-PBSA in Reproducing the Binding Free Energies to HIV-1 RT of TIBO Derivatives and Predicting the Binding Mode to HIV-1 RT of Efavirenz by Docking and MM-PBSA
inferredcites →https://doi.org/10.1021/ja00387a046openalex-snapshot
Molecular mechanics simulation of protein-ligand interactions: binding of thyroid hormone analogs to prealbumin
inferredcites →https://doi.org/10.1021/ja0104249openalex-snapshot
Binding Site Elucidation of Hydantoin-Based Antagonists of LFA-1 Using Multidisciplinary Technologies: Evidence for the Allosteric Inhibition of a Protein−Protein Interaction
inferredcites →https://doi.org/10.1021/ja034308copenalex-snapshot
Validation of a Model for the Complex of HIV-1 Reverse Transcriptase with Nonnucleoside Inhibitor TMC125
inferredcites →https://doi.org/10.1021/ja038496iopenalex-snapshot
A Quantum Mechanics-Based Scoring Function: Study of Zinc Ion-Mediated Ligand Binding
inferredcites →https://doi.org/10.1021/ja039847wopenalex-snapshot
Quantum Mechanical/Molecular Mechanical Investigation of the Mechanism of C−H Hydroxylation of Camphor by Cytochrome P450cam: Theory Supports a Two-State Rebound Mechanism
inferredcites →https://doi.org/10.1021/ja9621760openalex-snapshot
Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
inferredcites →https://doi.org/10.1021/jm00014a020openalex-snapshot
Prediction of Drug Binding Affinities by Comparative Binding Energy Analysis
inferredcites →https://doi.org/10.1021/jm000241hopenalex-snapshot
Binding of a Diverse Set of Ligands to Avidin and Streptavidin: An Accurate Quantitative Prediction of Their Relative Affinities by a Combination of Molecular Mechanics and Continuum Solvent Models
inferredcites →https://doi.org/10.1021/jm000255nopenalex-snapshot
Estimation of Binding Affinities for HEPT and Nevirapine Analogues with HIV-1 Reverse Transcriptase via Monte Carlo Simulations
inferredcites →https://doi.org/10.1021/jm00026a001openalex-snapshot
Computational Methods to Predict Binding Free Energy in Ligand-Receptor Complexes
inferredcites →https://doi.org/10.1021/jm00036a001openalex-snapshot
Applications of Combinatorial Technologies to Drug Discovery. 2. Combinatorial Organic Synthesis, Library Screening Strategies, and Future Directions
inferredcites →https://doi.org/10.1021/jm000405uopenalex-snapshot
Estimation of Binding Affinities for Selective Thrombin Inhibitors via Monte Carlo Simulations
inferredcites →https://doi.org/10.1021/jm001044lopenalex-snapshot
Protein-Based Virtual Screening of Chemical Databases. 1. Evaluation of Different Docking/Scoring Combinations
inferredcites →https://doi.org/10.1021/jm001070jopenalex-snapshot
Comparative Binding Energy (COMBINE) Analysis of Influenza Neuraminidase−Inhibitor Complexes
inferredcites →https://doi.org/10.1021/jm00145a002openalex-snapshot
A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
inferredcites →https://doi.org/10.1021/jm0100279openalex-snapshot
Are Free Energy Calculations Useful in Practice? A Comparison with Rapid Scoring Functions for the p38 MAP Kinase Protein System
inferredcites →https://doi.org/10.1021/jm0103256openalex-snapshot
Structure-Based Generation of a New Class of Potent Cdk4 Inhibitors: New de Novo Design Strategy and Library Design
inferredcites →https://doi.org/10.1021/jm010338jopenalex-snapshot
Molecular Dynamics and Free Energy Analyses of Cathepsin D−Inhibitor Interactions: Insight into Structure-Based Ligand Design
inferredcites →https://doi.org/10.1021/jm010548wopenalex-snapshot
Molecular Docking and High-Throughput Screening for Novel Inhibitors of Protein Tyrosine Phosphatase-1B
inferredcites →https://doi.org/10.1021/jm010580qopenalex-snapshot
Prediction of Activity for Nonnucleoside Inhibitors with HIV-1 Reverse Transcriptase Based on Monte Carlo Simulations
inferredcites →https://doi.org/10.1021/jm011002copenalex-snapshot
Structural Classification of Protein Kinases Using 3D Molecular Interaction Field Analysis of Their Ligand Binding Sites: Target Family Landscapes
inferredcites →https://doi.org/10.1021/jm020017nopenalex-snapshot
Molecular Properties That Influence the Oral Bioavailability of Drug Candidates
inferredcites →https://doi.org/10.1021/jm0209376openalex-snapshot
Theoretical Studies on the Inhibition Mechanism of Cyclooxygenase-2. Is There a Unique Recognition Site?
inferredcites →https://doi.org/10.1021/jm030137aopenalex-snapshot
Virtual Screening with Flexible Docking and COMBINE-Based Models. Application to a Series of Factor Xa Inhibitors
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Identification and Prediction of Promiscuous Aggregating Inhibitors among Known Drugs
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Lessons in Molecular Recognition: The Effects of Ligand and Protein Flexibility on Molecular Docking Accuracy
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A Specific Mechanism of Nonspecific Inhibition
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Evaluation of Docking Performance: Comparative Data on Docking Algorithms
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General Model for Estimation of the Inhibition of Protein Kinases Using Monte Carlo Simulations
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Conformational Analysis of Drug-Like Molecules Bound to Proteins: An Extensive Study of Ligand Reorganization upon Binding
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SYNOPSIS: SYNthesize and OPtimize System in Silico
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A Shape-Based 3-D Scaffold Hopping Method and Its Application to a Bacterial Protein−Protein Interaction
inferredcites →https://doi.org/10.1021/jm040180dopenalex-snapshot
Cytochrome P450 in Silico: An Integrative Modeling Approach
inferredcites →https://doi.org/10.1021/jm048957qopenalex-snapshot
The PDBbind Database: Methodologies and Updates
inferredcites →https://doi.org/10.1021/jm048972vopenalex-snapshot
Unveiling the Full Potential of Flexible Receptor Docking Using Multiple Crystallographic Structures
inferredcites →https://doi.org/10.1021/jm048973nopenalex-snapshot
Large-Scale Validation of a Quantum Mechanics Based Scoring Function: Predicting the Binding Affinity and the Binding Mode of a Diverse Set of Protein−Ligand Complexes
inferredcites →https://doi.org/10.1021/jm0492296openalex-snapshot
LEA3D: A Computer-Aided Ligand Design for Structure-Based Drug Design
inferredcites →https://doi.org/10.1021/jm0497343openalex-snapshot
A Combined QM/MM Approach to Protein−Ligand Interactions: Polarization Effects of the HIV-1 Protease on Selected High Affinity Inhibitors
inferredcites →https://doi.org/10.1021/jm049756popenalex-snapshot
Soft Docking and Multiple Receptor Conformations in Virtual Screening
inferredcites →https://doi.org/10.1021/jm049793gopenalex-snapshot
Toward a Pharmacophore for Kinase Frequent Hitters
inferredcites →https://doi.org/10.1021/jm049798dopenalex-snapshot
Comparison of Automated Docking Programs as Virtual Screening Tools
inferredcites →https://doi.org/10.1021/jm9602928openalex-snapshot
The Properties of Known Drugs. 1. Molecular Frameworks
inferredcites →https://doi.org/10.1021/jm970535bopenalex-snapshot
Comparative Binding Energy Analysis of HIV-1 Protease Inhibitors: Incorporation of Solvent Effects and Validation as a Powerful Tool in Receptor-Based Drug Design
inferredcites →https://doi.org/10.1021/jm980536jopenalex-snapshot
A General and Fast Scoring Function for Protein−Ligand Interactions: A Simplified Potential Approach
inferredcites →https://doi.org/10.1021/jm990352kopenalex-snapshot
Consensus Scoring: A Method for Obtaining Improved Hit Rates from Docking Databases of Three-Dimensional Structures into Proteins
inferredcites →https://doi.org/10.1021/jm990371uopenalex-snapshot
Predicting Relative Binding Free Energies of Tacrine−Huperzine A Hybrids as Inhibitors of Acetylcholinesterase§
inferredcites →https://doi.org/10.1021/jm9903996openalex-snapshot
Properties of Known Drugs. 2. Side Chains
inferredcites →https://doi.org/10.1021/jo960133wopenalex-snapshot
Tautomerism of Xanthine Oxidase Substrates Hypoxanthine and Allopurinol
inferredcites →https://doi.org/10.1023/a:1007996124545openalex-snapshot
Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
inferredcites →https://doi.org/10.1023/a:1007999920146openalex-snapshot
Prediction of binding constants of protein ligands: A fast method for the prioritization of hits obtained from de novo design or 3D database search programs
inferredcites →https://doi.org/10.1023/a:1011326914800openalex-snapshot
Comments on the design of chemical libraries for screening
inferredcites →https://doi.org/10.1023/a:1020155510718openalex-snapshot
A review of protein-small molecule docking methods
inferredcites →https://doi.org/10.1023/b:jcam.0000017496.76572.6fopenalex-snapshot
Comparative study of several algorithms for flexible ligand docking
inferredcites →https://doi.org/10.1023/b:jcam.0000021882.99270.4copenalex-snapshot
Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors
inferredcites →https://doi.org/10.1038/319199a0openalex-snapshot
Solvation energy in protein folding and binding
inferredcites →https://doi.org/10.1038/nature03197openalex-snapshot
Virtual screening of chemical libraries
inferredcites →https://doi.org/10.1038/nature03199openalex-snapshot
Simultaneous determination of protein structure and dynamics
inferredcites →https://doi.org/10.1038/nbt1059openalex-snapshot
A family of phosphodiesterase inhibitors discovered by cocrystallography and scaffold-based drug design
inferredcites →https://doi.org/10.1038/nrd1129openalex-snapshot
Implications of protein flexibility for drug discovery
inferredcites →https://doi.org/10.1038/nrd1343openalex-snapshot
Small-molecule inhibitors of protein–protein interactions: progressing towards the dream
inferredcites →https://doi.org/10.1038/nrd941openalex-snapshot
Integration of virtual and high-throughput screening
inferredcites →https://doi.org/10.1039/b309040jopenalex-snapshot
Research applications of the Cambridge Structural Database (CSD)
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Biological spectra analysis: Linking biological activity profiles to molecular structure
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Ab initio quantum chemistry: Methodology and applications
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Protein–protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces
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History, Evolution, and Trends in Compound Management for High Throughput Screening
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The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data
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Electrostatic effects in proteins: comparison of dielectric and charge models
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A new method for predicting binding affinity in computer-aided drug design
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New challenges in quantum chemistry: quests for accurate calculations for large molecular systems
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The Uppsala Electron-Density Server
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DIRECT SOLUTION OF THE POISSON EQUATION FOR BIOMOLECULES OF ARBITRARY SHAPE, POLARIZABILITY DENSITY, AND CHARGE DISTRIBUTION
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The Protein Kinase Complement of the Human Genome
inferredcites →https://doi.org/10.1126/science.1096361openalex-snapshot
The Many Roles of Computation in Drug Discovery
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Generation of an LFA-1 Antagonist by the Transfer of the ICAM-1 Immunoregulatory Epitope to a Small Molecule
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