yusuke1997/dblp-id-title huggingface dataset:
Allosteric Mechanism of the Hsp90 Chaperone Interactions with Cochaperones and Client Proteins by Modulating Communication Spines of Coupled Regulatory Switches: Integrative Atomistic Modeling of Hsp90 Signaling in Dynamic Interaction Networks
Development of Neural Network QSPR Models for Hansch Substituent Constants. 1. Method and Validations
HybridDock: A Hybrid Protein-Ligand Docking Protocol Integrating Protein- and Ligand-Based Approaches
p38α Kinase Auto-Activation through Its Conformational Transition Induced by Tyr323 Phosphorylation
Dynamic Profiling of β-Coronavirus 3CL Mpro Protease Ligand-Binding Sites
Development and Testing of Druglike Screening Libraries
Distribution of K, the number of Kekule structures, in benzenoid hydrocarbons: normal benzenoids with K up to 110
Automatic Perception of Organic Molecules Based on Essential Structural Information
Modular Architecture of Metabolic Pathways Revealed by Conserved Sequences of Reactions
Identification, Synthesis, and Biological Evaluations of Potent Inhibitors Targeting Type I Protein Arginine Methyltransferases
Matching two-dimensional chemical graphs using genetic algorithms
Prediction of Critical Temperatures and Pressures of Industrially Important Organic Compounds from Molecular Structure
Partitioning of Benzoic Acid into 1, 2-Dimyristoyl-sn-glycero-3-phosphocholine and Blood-Brain Barrier Mimetic Bilayers
Structure-Based Predictions of 1 H NMR Chemical Shifts Using Feed-Forward Neural Networks
Peak Alignment of Urine NMR Spectra Using Fuzzy Warping
Nearest Neighbor Search in General Metric Spaces Using a Tree Data Structure with a Simple Heuristic
Interpretation of the Binding Affinities of PTP1B Inhibitors with the MM-GB/SA Method and the X-Score Scoring Function
Ring Repeating Unit: An Upgraded Structure Representation of Linear Condensation Polymers for Property Prediction
A Catalogue of Growth Transformations of Fullerene Polyhedra
Molecular Structure Extraction from Documents Using Deep Learning
A New Modular Architecture for Chemical Structure Elucidation Systems
Simulated Epidemics in 3D Protein Structures to Detect Functional Properties
Membrane Permeability in Cyclic Peptides is Modulated by Core Conformations
Tios: The Internet of Simulations. Turning Molecular Dynamics into a Data Streaming Web Application
DiMSim: A Discrete-Event Simulator of Metabolic Networks
Method for generating a chemical reaction index for storage and retrieval of information. Comments
CHARMMing: A New, Flexible Web Portal for CHARMM
Prediction of Polar Surface Area and Drug Transport Processes Using Simple Parameters and PLS Statistics
Autoparty: Machine Learning-Guided Visual Inspection of Molecular Docking Results
Simulation Foundry: Automated and F.A.I.R. Molecular Modeling
HyperChem, release 2: molecular modeling for the personal computer
Discovery of Chemokine CXCL12 Inhibitors by Tandem Application of Virtual Screening and NMR Spectrometry
Integration of chemical history into the chemical literature course
Nanopolysaccharide Builder: A User-Friendly Tool for Atomistic Models of Polysaccharide-Based Nanostructures
Condensed Representation of DNA Primary Sequences
Molecular identification number for substructure searches
Shannon Entropy-Based Fingerprint Similarity Search Strategy
How Well Does the Extended Linear Interaction Energy Method Perform in Accurate Binding Free Energy Calculations?
Opinion Mining by Convolutional Neural Networks for Maximizing Discoverability of Nanomaterials
Delta Machine Learning to Improve Scoring-Ranking-Screening Performances of Protein-Ligand Scoring Functions
ELDAR, a knowledge base system on microcomputer for electrolyte solutions. The factual knowledge of ELDAR
Prediction of Aqueous Solubility and Partition Coefficient Optimized by a Genetic Algorithm Based Descriptor Selection Method
Improved Prediction of Drug-Protein Interactions through Physics-Based Few-Shot Learning
Advances and Challenges in De Novo Drug Design Using Three-Dimensional Deep Generative Models
The Role of Chemical Information Science in Computer-Assisted Chemical Research
Molecular Mechanics and Conformational Analysis in Drug Design By Gyorgy Keseru and Istvan Kolossvary. Blackwell Science Ltd., Oxford, UK, 1999, 168 pp, ISBN 0-632-05289-9
Brief Comparison between Experimental and Computationally Generated Ensembles of RNA Dinucleotides
GA Strategy for Variable Selection in QSAR Studies: GA-Based PLS Analysis of Calcium Channel Antagonists
In Silico Identification of JMJD3 Demethylase Inhibitors
Transfer-Learning Deep Raman Models Using Semiempirical Quantum Chemistry
Systematic Modeling of log D7.4 Based on Ensemble Machine Learning, Group Contribution, and Matched Molecular Pair Analysis
Unraveling Activation-Related Rearrangements and Intrinsic Divergence from Ligand-Specific Conformational Changes of the Dopamine D3 and D2 Receptors
Generative Deep Learning for Targeted Compound Design
Phosphoinositide-3-kinases (PI3Ks): Combined Comparative Modeling and 3D-QSAR To Rationalize the Inhibition of p110α
Comparative Assessment of Water Models in Protein-Glycan Interaction: Insights from Alchemical Free Energy Calculations and Molecular Dynamics Simulations
Discovery of Multitarget-Directed Ligands against Alzheimer's Disease through Systematic Prediction of Chemical-Protein Interactions
Conserved Water Networks Identification for Drug Design Using Density Clustering Approaches on Positional and Orientational Data
Intraresidual Correlated Motions in Peptide Chains
GROMACS in the Cloud: A Global Supercomputer to Speed Up Alchemical Drug Design
N -Tosyl Hydrazone Benzopyran, a New Ligand of PPARα Obtained from Mapping the Conformational Space of Its Active Site
QM/MM As a Tool in Fragment Based Drug Discovery. A Cross-Docking, Rescoring Study of Kinase Inhibitors
Inferring Lifetime Distributions from Kinetics by Maximizing Entropy Using a Bootstrapped Model
MQN-Mapplet: Visualization of Chemical Space with Interactive Maps of DrugBank, ChEMBL, PubChem, GDB-11, and GDB-13
Higher-Order Weighted Perturbation-Based Multilevel Information Fusion Model for Predicting CircRNA-Disease Associations
Personalized Energy Adaptation through Reweighting Learning (PEARL) Force Field for Intrinsically Disordered Proteins
Molecular Diversity and Representativity in Chemical Databases
Xenon Explores Apparent and Cryptic Binding Sites
The Effect of Microwaves on Protein Structure: Molecular Dynamics Approach
When Does Additional Information Improve Accuracy of RNA Secondary Structure Prediction?
Cosolvent-Based Protein Pharmacophore for Ligand Enrichment in Virtual Screening
CorrEA: A Web Server for Optimizing Correlations between Calculated Energies and Activities in Ligand-Receptor Systems Considering Multiple Binding Site Conformations
KUTE: Green-Kubo Uncertainty-Based Transport Coefficient Estimator
Comments on the Article "Evaluation of p K a Estimation Methods on 211 Druglike Compounds"
Prediction of Acrylonitrile-Butadiene-Styrene Mechanical Properties through Compressed-Sensing Techniques
Unlocking the Binding and Reaction Mechanism of Hydroxyurea Substrates as Biological Nitric Oxide Donors
A Machine Learning-Based Method To Improve Docking Scoring Functions and Its Application to Drug Repurposing
WebMolCS: A Web-Based Interface for Visualizing Molecules in Three-Dimensional Chemical Spaces
Combined Virtual Screening and Substructure Search for Discovery of Novel FABP4 Inhibitors
Interpretation of Nonlinear QSAR Models Applied to Ames Mutagenicity Data
Computing the Pathogenicity of Alzheimer's Disease Presenilin 1 Mutations
Binding Sites of Bicarbonate in Phosphoenolpyruvate Carboxylase
Predicting Skin Permeability by Means of Computational Approaches: Reliability and Caveats in Pharmaceutical Studies
GPU Accelerated Support Vector Machines for Mining High-Throughput Screening Data
Evidence That Less Can Be More for Transferable Force Fields
Molecular Modeling of the Peptide Agonist-Binding Site in a Neurokinin-2 Receptor
Topliss Batchwise Schemes Reviewed in the Era of Open Data Reveal Significant Differences between Enzymes and Membrane Receptors
Benchmarking Commercial Conformer Ensemble Generators
Comparative Study of Deep Generative Models on Chemical Space Coverage
ThermoData Engine (TDE): Software Implementation of the Dynamic Data Evaluation Concept. 6. Dynamic Web-Based Data Dissemination through the NIST Web Thermo Tables
Consensus Pharmacological Interactions for PLK2 Inhibitor Identification in Colorectal Cancer Treatment
Predicting Critical Properties and Acentric Factors of Fluids Using Multitask Machine Learning
CCD2MD: A Suite of Packages for Preparing Co-Folded Outputs for Molecular Dynamics Simulations
Integrating Protein Language Models and Geometric Deep Learning for Peptide Toxicity Prediction
ncRNA Coding Potential Prediction Using BiLSTM and Transformer Encoder-Based Model
Neural Network Studies. 3. Variable Selection in the Cascade-Correlation Learning Architecture
Bounds for the Schultz Molecular Topological Index of Benzenoid Systems in Terms of the Wiener Index
Activity Models of Key GPCR Families in the Central Nervous System: A Tool for Many Purposes
Classification of Cyclooxygenase-2 Inhibitors Using Support Vector Machine and Random Forest Methods
Training a Scoring Function for the Alignment of Small Molecules
Assay Related Target Similarity (ARTS) - Chemogenomics Approach for Quantitative Comparison of Biological Targets
Spectral Moments of Polyacenes
A Semantic Web Ontology for Small Molecules and Their Biological Targets
PROTACable Is an Integrative Computational Pipeline of 3-D Modeling and Deep Learning To Automate the De Novo Design of PROTACs
Molecular Docking Characterizes Substrate-Binding Sites and Efflux Modulation Mechanisms within P-Glycoprotein
Evaluation of Binary QSAR Models Derived from LUDI and MOE Scoring Functions for Structure Based Virtual Screening
Protein-Ligand Binding Free Energy Calculation by the Smooth Reaction Path Generation (SRPG) Method
Quasi-orthogonal Basis Sets of Molecular Graph Descriptors as a Chemical Diversity Measure
Evaluations of the Perturbation Resistance of the Deep-Learning-Based Ligand Conformation Optimization Algorithm
The Three-Dimensional Cycle Index of the Leapfrog of a Polyhedron
Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method
End-Point Affinity Estimation of Galectin Ligands by Classical and Semiempirical Quantum Mechanical Potentials
The Importance of Local Chemical Structure for Chemical Metabolism by Human Uridine 5'-Diphosphate-Glucuronosyltransferase
SCAM Detective: Accurate Predictor of Small, Colloidally Aggregating Molecules
A Simplified Algorithm Using Base 5 Numbers to Assign Canonical Names to Cata-Condensed Benzenoid Polybenzenes. [Erratum to document cited in CA120: 297668]
Note on Naive Bayes Based on Binary Descriptors in Cheminformatics
Structure-Based Rational Screening of Novel Hit Compounds with Structural Diversity for Cytochrome P450 Sterol 14α-Demethylase from Penicillium digitatum
Dissecting the Structural Plasticity and Dynamics of Cytochrome P450 2B4 by Molecular Dynamics Simulations
Automated conformational analysis and structure generation: algorithms for molecular perception
PatchSearch: A Fast Computational Method for Off-Target Detection
Comprehensive Assessment of BERT-Based Methods for Predicting Antimicrobial Peptides
Economic Aspects of Chemical Information
Findings of the Second Challenge to Predict Aqueous Solubility
Machine Learning Methodologies Applied to Magnetocaloric Perovskites Discovery
Efficiency of Stratification for Ensemble Docking Using Reduced Ensembles
Searching for Structure: Characterizing the Protein Conformational Landscape with Clustering-Based Algorithms
Benchmarking Data Sets for the Evaluation of Virtual Ligand Screening Methods: Review and Perspectives
DEM-Based Approach for the Modeling of Gelation and Its Application to Alginate
Numerical databases on materials property data at CINDAS/Purdue University
charmm2gmx: An Automated Method to Port the CHARMM Additive Force Field to GROMACS
GUI Implementation of VCDtools, A Program to Analyze Computed Vibrational Circular Dichroism Spectra
Quantitative Structure-Activity Relationship of Flavonoid p56lck Protein Tyrosine Kinase Inhibitors. A Neural Network Approach
Delineating the Ligand-Receptor Interactions That Lead to Biased Signaling at the μ-Opioid Receptor
Distance Matrixes Yielding Angles between Arcs of the Graphs
Similarity Searching in Databases of Flexible 3D Structures Using Smoothed Bounded Distance Matrices
Prediction of Aptamer-Small-Molecule Interactions Using Metastable States from Multiple Independent Molecular Dynamics Simulations
Post-Translational Modifications at the Coarse-Grained Level with the SIRAH Force Field
Formulation Graphs for Mapping Structure-Composition of Battery Electrolytes to Device Performance
Are Protein Conformational Ensembles in Agreement with Experimental Data? A Geometrical Interpretation of the Problem
Virtual Screening of Molecular Databases Using a Support Vector Machine
Discovery of Novel Small-Molecule Inhibitors of SARS-CoV-2 Main Protease as Potential Leads for COVID-19 Treatment
Specialty Chemicals Electronic Source Book, 1997 Edition on CD-ROM
Unraveling the Allosteric Communication Mechanisms in T-Cell Receptor-Peptide-Loaded Major Histocompatibility Complex Dynamics Using Molecular Dynamics Simulations: An Approach Based on Dynamic Cross Correlation Maps and Residue Interaction Energy Calculations
Effect of a pH Gradient on the Protonation States of Cytochrome c Oxidase: A Continuum Electrostatics Study
RIGR: Resonance-Invariant Graph Representation for Molecular Property Prediction
Improving Predictive Efficacy for Drug Resistance in Novel HIV-1 Protease Inhibitors through Transfer Learning Mechanisms
Locating Sweet Spots for Screening Hits and Evaluating Pan-Assay Interference Filters from the Performance Analysis of Two Lead-like Libraries
Modeling Ligand-Receptor Interaction for Some MHC Class II HLA-DR4 Peptide Mimetic Inhibitors Using Several Molecular Docking and 3D QSAR Techniques
Enhancing Machine Learning Potentials through Transfer Learning across Chemical Elements
Boosting Drug-Disease Association Prediction for Drug Repositioning via Dual-Feature Extraction and Cross-Dual-Domain Decoding
Mechanistic Insights into Passive Membrane Permeability of Drug-like Molecules from a Weighted Ensemble of Trajectories
Introducing the Automated Ligand Searcher
The Toxicology Data Bank
QSAR Comparative Study of Wiener Descriptors for Weighted Molecular Graphs
Alchemical Calculation of Relative Free Energies for Charge-Changing Mutations at Protein-Protein Interfaces Considering Fixed and Variable Protonation States
Pre-Exascale Computing of Protein-Ligand Binding Free Energies with Open Source Software for Drug Design
A Data Mining Method To Facilitate SAR Transfer
Combining Molecular Dynamics and Machine Learning to Predict Self-Solvation Free Energies and Limiting Activity Coefficients
Solvent-Specific Featurization for Predicting Free Energies of Solvation through Machine Learning
Dissecting Kinase Profiling Data to Predict Activity and Understand Cross-Reactivity of Kinase Inhibitors
Use of 3D QSAR Models for Database Screening: A Feasibility Study
Object-oriented programming applied to laboratory automation. 2. The object-oriented Chemical Information Manager for the Analytical Director
Novel Approach for Efficient Pharmacophore-Based Virtual Screening: Method and Applications
Functional Loop Dynamics and Characterization of the Inactive State of the NS2B-NS3 Dengue Protease due to Allosteric Inhibitor Binding
Fragment Search in Acyclic Structures
On-Line Storage and Retrieval of Chemical Information. I. Structure Entry
Influence of Data Curation and Confidence Levels on Compound Predictions Using Machine Learning Models
Estimating the Vertical Ionization Potential of Single-Stranded DNA Molecules
Amber-Compatible Parametrization Procedure for Peptide-like Compounds: Application to 1, 4- and 1, 5-Substituted Triazole-Based Peptidomimetics
Molcontroller: A VMD Graphical User Interface Featuring Molecule Manipulation
Correction to "ROSHAMBO2: Accelerating Molecular Alignment for Large Chemical Libraries with GPU Optimization and Algorithmic Advances"
metaCDA: A Novel Framework for CircRNA-Driven Drug Discovery Utilizing Adaptive Aggregation and Meta-Knowledge Learning
Topology of Membrane Proteins
A Robust Boosting Regression Tree with Applications in Quantitative Structure-Activity Relationship Studies of Organic Compounds
Structure- and Ligand-Based Virtual Screening on DUD-E+: Performance Dependence on Approximations to the Binding Pocket
Ab Initio Quantum Molecular Similarity Measures on Metal-Substituted Carbonic Anhydrase (MIICA, M = Be, Mg, Mn, Co, Ni, Cu, Zn, and Cd)
RiSKs in Computational Modeling of Isoform-Selective RSK Inhibitors
Mechanism of Dynamic Binding of Replication Protein A to ssDNA
SmartChemist─Simplifying Communication About Organic Chemical Structures
Multisolvent Similarity Measure of Chinese Herbal Medicine Ingredients for Cold-Hot Nature Identification
Nonadditivity Analysis
Software Review of ChemBioDraw 12.0
Optimization of Molecular Representativeness
Protein-Ligand Complex Solvation Thermodynamics: Development, Parameterization, and Testing of GIST-Based Solvent Functionals
AtomVision: A Machine Vision Library for Atomistic Images
Lead Discovery of SARS-CoV-2 Main Protease Inhibitors through Covalent Docking-Based Virtual Screening
Solvation Free Energies of Small Amines: An Interpretation Thereof and Its General Significance
BALLDock/SLICK: A New Method for Protein-Carbohydrate Docking
Pharmacophore Modeling, Virtual Screening, and in Vitro Testing Reveal Haloperidol, Eprazinone, and Fenbutrazate as Neurokinin Receptors Ligands
Boosting Docking-Based Virtual Screening with Deep Learning
GLA-Synergy: An Interpretable Global-Local Adaptive Framework for Drug Synergy Prediction in Cancer Treatment
Magnetic Water Treatment for a Less Tenacious Scale
Annotation of Allosteric Compounds to Enhance Bioactivity Modeling for Class A GPCRs
Development and Evaluation of an Integrated Virtual Screening Strategy by Combining Molecular Docking and Pharmacophore Searching Based on Multiple Protein Structures
Eliciting Possible Reaction Equations and Metabolic Pathways Involving Orphan Metabolites
Effect of Molecular Orientational Correlations on Solvation Free Energy Computed by Reference Interaction Site Model Theory
HlightReaxMD: A Machine Learning-Augmented Multiscale Analysis Framework for Radiation Chemistry Dynamics and Damage Prediction
Large-Scale Virtual Screening for the Discovery of SARS-CoV-2 Papain-like Protease (PLpro) Non-covalent Inhibitors
KDEEP: Protein-Ligand Absolute Binding Affinity Prediction via 3D-Convolutional Neural Networks
Improved Indexing of Chemical Abstracts Service Post-Treated Polymers
Key Residues in δ Opioid Receptor Allostery Explored by the Elastic Network Model and the Complex Network Model Combined with the Perturbation Method
Organization of Scientific and Technical Information in Hungary
Extended Adjacency Matrix Indices and Their Applications
Can Pretrained Models Really Learn Better Molecular Representations for AI-Aided Drug Discovery?
InsectiPAD: A Web Tool Dedicated to Exploring Physicochemical Properties and Evaluating Insecticide-Likeness of Small Molecules
Prediction of Transcription Factor Binding Sites on Cell-Free DNA Based on Deep Learning
Machine Learning Algorithm Identifies an Antibiotic Vocabulary for Permeating Gram-Negative Bacteria
Optimizing the Multivalent Binding of the Bacterial Lectin LecA by Glycopeptide Dendrimers for Therapeutic Purposes
Characterizing Binding of Small Molecules. II. Evaluating the Potency of Small Molecules to Combat Resistance Based on Docking Structures
Spectral Encoder to Extract the Features of Near-Infrared Spectra for Multivariate Calibration
Ligand Many-Body Expansion as a General Approach for Accelerating Transition Metal Complex Discovery
Computing the Volume, Surface Area, Mean, and Gaussian Curvatures of Molecules and Their Derivatives
Kekule patterns and Clar patterns in bipartite plane graphs
Chemoinformatics-Based Classification of Prohibited Substances Employed for Doping in Sport
An Efficient Design for Chemical Structure Searching. II. The File Oraganization
Materials Dual-Source Knowledge Retrieval-Augmented Generation for Local Large Language Models in Photocatalysts
A New Statistical Approach to Predicting Aromatic Hydroxylation Sites. Comparison with Model-Based Approaches
The NIH-EPA Structure and Nomenclature Search System
Predicting Protein-Peptide Complex Structures by Accounting for Peptide Flexibility and the Physicochemical Environment
Comparative Study of Molecular Mechanics Force Fields for β-Peptidic Foldamers: Folding and Self-Association
Can we predict reactivity using MO calculations?
QuantumScents: Quantum-Mechanical Properties for 3.5k Olfactory Molecules
SCScore: Synthetic Complexity Learned from a Reaction Corpus
A Comparative Insight into Amprenavir Resistance of Mutations V32I, G48V, I50V, I54V, and I84V in HIV-1 Protease Based on Thermodynamic Integration and MM-PBSA Methods
Spectra Estimation for Computer-Aided Structure Determination
Database Development in a Regulatory Agency
IDC Inorganic Chemicals Data Base. 2. Utilization of Chemical Abstracts Service databases for the IDC inorganic chemistry documentation system
The Development and Compilation of Chemical Information by the Bureau of Drugs Medical Library for the Drug Review Process
Molecular Mechanism of Nucleosome Recognition by the Pioneer Transcription Factor Sox
On Three-Electron Bonds and Hydrogen Bonds in the Open-Shell Complexes [H 2 X 2 ] + for X = F, Cl, and Br †
Parametrization of Nonbonded Force Field Terms for Metal-Organic Frameworks Using Machine Learning Approach
TransfIGN: A Structure-Based Deep Learning Method for Modeling the Interaction between HLA-A*02:01 and Antigen Peptides
Searching the literature to learn how the term ligand became a part of the chemical language
Backbone Alignment Modeling of the Structure-Activity Relationships of Opioid Ligands
Exploring Chemical Rings in a Simple Topological-Descriptor Space
Semiconductor Journals
Atom-Centered Interacting Fragments and Similarity Search Applications
Fillers, Extenders, and Diluents Electronic Handbook
Algorithm for the Direct Enumeration of Chiral and Achiral Skeletons of a Homosubstituted Derivative of a Monocyclic Cycloalkane with a Large and Factorizable Ring Size n
Data Compression in Digital Systems By Roy Hoffman. Digital Multimedia Standards Series. International Thomson Publishing/Chapman & Hall: New York, 1996, 415 pp, ISBN 0-412-08551-8
MEMO-Stab2: Multi-View Sequence-Based Deep Learning Framework for Predicting Mutation-Induced Stability Changes in Transmembrane Proteins
CELLmicrocosmos 2.2 MembraneEditor: A Modular Interactive Shape-Based Software Approach To Solve Heterogeneous Membrane Packing Problems
QSAR Study of Antimicrobial Activity of Some 3-Nitrocoumarins and Related Compounds
ReactionMap: An Efficient Atom-Mapping Algorithm for Chemical Reactions
Debunking the Idea that Ligand Efficiency Indices Are Superior to pIC50 as QSAR Activities
Wrapping Up Viruses at Multiscale Resolution: Optimizing PACKMOL and SIRAH Execution for Simulating the Zika Virus
Characterization, in Vivo Evaluation, and Molecular Modeling of Different Propofol-Cyclodextrin Complexes To Assess Their Drug Delivery Potential at the Blood-Brain Barrier Level
Vertex-Edge-Weighted Molecular Graphs: A Study on Topological Indices and Their Relevance to Physicochemical Properties of Drugs Used in Cancer Treatment
Substructure-Based Support Vector Machine Classifiers for Prediction of Adverse Effects in Diverse Classes of Drugs
Prediction of Aqueous Solubility for a Diverse Set of Heteroatom-Containing Organic Compounds Using a Quantitative Structure-Property Relationship
Can Reasoning Power Significantly Improve the Knowledge of Large Language Models for Chemistry?─Based on Conversations with LLMs
The Local Minima Method (LMM) of Pharmacophore Determination: A Protocol for Predicting the Bioactive Conformation of Small, Conformationally Flexible Molecules