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A Knowledge-Based Energy Function for Protein−Ligand, Protein−Protein, and Protein−DNA Complexes
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Outgoing claims: the papers this work cites, builds on, or argues with.
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Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
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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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Influence of protein structure databases on the predictive power of statistical pair potentials
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Structure-based prediction of DNA target sites by regulatory proteins
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Use of pair potentials across protein interfaces in screening predicted docked complexes
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Principles and Methods of Docking and Ligand Design
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Energetics of the specific binding interaction of the first three zinc fingers of the transcription factor TFIIIA with its cognate DNA sequence
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Thermodynamic databases for proteins and protein-nucleic acid interactions
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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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A single amino acid in the SH3 domain of Hck determines its high affinity and specificity in binding to HIV‐1 Nef protein.
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Two heads are better than one: crystal structure of the insect derived double domain Kazal inhibitor rhodniin in complex with thrombin.
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Validation of the general purpose tripos 5.2 force field
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Calculation of the free energy of association for protein complexes
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Binding of amino acid side chains to preformed cavities: Interaction of serine proteinases with turkey ovomucoid third domains with coded and noncoded P1 residues
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A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design
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Participation of water in hin recombinase‐DNA recognition
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Potential of mean force for protein–protein interaction studies
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CAPRI: A Critical Assessment of PRedicted Interactions
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Critical assessment of methods of protein structure prediction (CASP)-round V
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Quantifying the effect of burial of amino acid residues on protein stability
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Single‐body residue‐level knowledge‐based energy score combined with sequence‐profile and secondary structure information for fold recognition
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A physical reference state unifies the structure‐derived potential of mean force for protein folding and binding
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Affinity and Specificity of Serine Endopeptidase-Protein Inhibitor Interactions
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Thermodynamic Investigation of Hirudin Binding to the Slow and Fast Forms of Thrombin: Evidence for Folding Transitions in the Inhibitor and Protease Coupled to Binding
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Statistical Potentials Extracted From Protein Structures: How Accurate Are They?
inferredcites →https://doi.org/10.1006/jmbi.1996.0477openalex-snapshot
A Fast Flexible Docking Method using an Incremental Construction Algorithm
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Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen
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Thermodynamics of the interactions of Lac repressor with variants of the symmetric Lac operator: effects of converting a consensus site to a non-specific site
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The mechanism of an inhibitory antibody on TF-initiated blood coagulation revealed by the crystal structures of human tissue factor, Fab 5G9 and TF·5G9 complex 1 1Edited by D. C. Rees
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Thermodynamic characterization of non-sequence-specific DNA-binding by the Sso7d protein from Sulfolobus solfataricus
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Structural and functional analysis of the 1:1 growth hormone:receptor complex reveals the molecular basis for receptor affinity
inferredcites →https://doi.org/10.1006/jmbi.1998.1743openalex-snapshot
The effects of salt on the TATA binding protein-DNA interaction from a hyperthermophilic archaeon
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Determination of the binding constants for three HPr-specific monoclonal antibodies and their Fab fragments
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A quantitative UV laser footprinting analysis of the interaction of IHF with specific binding sites: re-evaluation of the effective concentration of IHF in the cell
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Probing the physical basis for trp repressor-operator recognition
inferredcites →https://doi.org/10.1006/jmbi.1999.3371openalex-snapshot
Knowledge-based scoring function to predict protein-ligand interactions
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Conformational Changes and Cleavage by the Homing Endonuclease I-PpoI: A Critical Role for a Leucine Residue in the Active Site
inferredcites →https://doi.org/10.1006/jmbi.2000.3888openalex-snapshot
Major Groove Recognition by Three-stranded β-Sheets: Affinity Determinants and Conserved Structural Features
inferredcites →https://doi.org/10.1006/jmbi.2000.4428openalex-snapshot
The energetics of the interaction of BamHI endonuclease with its recognition site GGATCC11Edited by R. Ebright
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DNA binding and cleavage selectivity of the Escherichia coli DNA G:T-mismatch endonuclease (vsr protein) 1 1Edited by J. Karn
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A knowledge-based scoring function for protein-ligand interactions: Probing the reference state
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The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
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Binding constants for a physiologic electron-transfer protein complex between methylamine dehydrogenase and amicyanin. Effects of ionic strength and bound copper on binding
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Pre‐existence of the active site in zymogens, the interaction of trypsinogen with the basic pancreatic trypsin inhibitor (Kunitz)
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Thermodynamics of gelation of sickle cell deoxyhemoglobin
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Binding of the bovine pancreatic secretory trypsin inhibitor (Kazal) to bovine serine (pro)enzymes
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Synthetic peptides as the basis for vaccine design
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Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming
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Intermolecular and Intramolecular Readout Mechanisms in Protein–DNA Recognition
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Development of Unified Statistical Potentials Describing Protein-Protein Interactions
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Effects of nucleoside analog incorporation on DNA binding to the DNA binding domain of the GATA‐1 erythroid transcription factor
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Glu192–>Gln substitution in thrombin yields an enzyme that is effectively inhibited by bovine pancreatic trypsin inhibitor and tissue factor pathway inhibitor
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Streptococcal protein G. Gene structure and protein binding properties.
inferredcites →https://doi.org/10.1016/s0021-9258(18)53178-1openalex-snapshot
Bovine stefin C, a new member of the stefin family.
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Specificity of Protein–DNA Recognition Revealed by Structure-based Potentials: Symmetric/Asymmetric and Cognate/Non-cognate Binding
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Calculation of conformational ensembles from potentials of mena force
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[58] Carboxypeptidase inhibitor from potatoes
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[61] The broad-specificity proteinase inhibitor 5 II from the sea anemone Anemonia sulcata
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Crystal Structure of the Conserved Core of HIV-1 Nef Complexed with a Src Family SH3 Domain
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Crystal Structure of Human Cyclophilin A Bound to the Amino-Terminal Domain of HIV-1 Capsid
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How and why phosphotyrosine-containing peptides bind to the SH2 and PTB domains
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Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models
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Thermodynamic Evaluation of Binding Interactions in the Methionine Repressor System of Escherichia coli using Isothermal Titration Calorimetry
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Calorimetric Analysis of .lambda. cI Repressor Binding to DNA Operator Sites
inferredcites →https://doi.org/10.1021/bi000342hopenalex-snapshot
Stopped-Flow Fluorescence Studies of HMG-Domain Protein Binding to Cisplatin-Modified DNA
inferredcites →https://doi.org/10.1021/bi000377hopenalex-snapshot
Characterization of Sequence-Specific DNA Binding by the Transcription Factor Oct-1
inferredcites →https://doi.org/10.1021/bi0004495openalex-snapshot
Enhanced Binding of the TATA-Binding Protein to TATA Boxes Containing Flanking Cisplatin 1,2-Cross-Links
inferredcites →https://doi.org/10.1021/bi00070a015openalex-snapshot
Thermodynamics of the glucocorticoid receptor-DNA interaction: Binding of wild-type GR DBD to different response elements
inferredcites →https://doi.org/10.1021/bi00074a008openalex-snapshot
Directed mutagenesis and barnase-barstar recognition
inferredcites →https://doi.org/10.1021/bi00113a014openalex-snapshot
Effects of surface amino acid replacements in cytochrome c peroxidase on complex formation with cytochrome c
inferredcites →https://doi.org/10.1021/bi00113a015openalex-snapshot
Kinetics of extension of O6-methylguanine paired with cytosine or thymine in defined oligonucleotide sequences
inferredcites →https://doi.org/10.1021/bi001174wopenalex-snapshot
Interaction of the Escherichia coli Replication Terminator Protein (Tus) with DNA: A Model Derived from DNA-Binding Studies of Mutant Proteins by Surface Plasmon Resonance
inferredcites →https://doi.org/10.1021/bi00162a004openalex-snapshot
Structure of the hirulog 3-thrombin complex and nature of the S' subsites of substrates and inhibitors
inferredcites →https://doi.org/10.1021/bi00192a002openalex-snapshot
N9 Neuraminidase Complexes with Antibodies NC41 and NC10: Empirical Free Energy Calculations Capture Specificity Trends Observed with Mutant Binding Data
inferredcites →https://doi.org/10.1021/bi0028643openalex-snapshot
Ion Concentration and Temperature Dependence of DNA Binding: Comparison of PurR and LacI Repressor Proteins
inferredcites →https://doi.org/10.1021/bi00483a001openalex-snapshot
Dominant forces in protein folding
inferredcites →https://doi.org/10.1021/bi015979vopenalex-snapshot
Determinants in the Sequence Specific Binding of Two Plant Transcription Factors, CBF1 and NtERF2, to the DRE and GCC Motifs
inferredcites →https://doi.org/10.1021/bi952363vopenalex-snapshot
Substrate Binding and Turnover by the Highly Specific I-PpoI Endonuclease
inferredcites →https://doi.org/10.1021/bi952555qopenalex-snapshot
Equilibrium DNA Binding of Sac7d Protein from the HyperthermophileSulfolobus acidocaldarius: Fluorescence and Circular Dichroism Studies,
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Coupled Folding and Site-Specific Binding of the GCN4-bZIP Transcription Factor to the AP-1 and ATF/CREB DNA Sites Studied by Microcalorimetry
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Energetics of Folding and DNA Binding of the MATα2 Homeodomain
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Probing Intermolecular Main Chain Hydrogen Bonding in Serine Proteinase−Protein Inhibitor Complexes: Chemical Synthesis of Backbone-Engineered Turkey Ovomucoid Third Domain
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Cation-Promoted Association of Escherichia coli Phosphocarrier Protein IIAGlc with Regulatory Target Protein Glycerol Kinase: Substitutions of a Zinc(II) Ligand and Implications for Inducer Exclusion
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Comparison of the DNA Binding Characteristics of the Related Zinc Finger Proteins WT1 and EGR1
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Mechanism of DNA Binding Enhancement by Hepatitis B Virus Protein pX
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Thermodynamics of the DNA Binding Reaction of Transcription Factor MASH-1
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Quantitative Hydroxyl Radical Footprinting Reveals Cooperative Interactions between DNA-Binding Subdomains of PU.1 and IRF4
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Substitutions at Histidine 74 and Aspartate 278 Alter Ligand Binding and Allostery in Lactose Repressor Protein
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Protein−Protein Interactions: Interface Structure, Binding Thermodynamics, and Mutational Analysis
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SMoG: de Novo Design Method Based on Simple, Fast, and Accurate Free Energy Estimates. 1. Methodology and Supporting Evidence
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SMall Molecule Growth 2001 (SMoG2001): An Improved Knowledge-Based Scoring Function for Protein−Ligand Interactions
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Comparative Evaluation of 11 Scoring Functions for Molecular Docking
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Comparative Binding Energy (COMBINE) Analysis of OppA−Peptide Complexes to Relate Structure to Binding Thermodynamics
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A General and Fast Scoring Function for Protein−Ligand Interactions: A Simplified Potential Approach
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Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
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DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
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Further development and validation of empirical scoring functions for structure-based binding affinity prediction
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Binding activities of a repertoire of single immunoglobulin variable domains secreted from Escherichia coli
inferredcites →https://doi.org/10.1038/341546a0openalex-snapshot
Protease nexin-II, a potent anti-chymotrypsin, shows identity to amyloid β-protein precursor
inferredcites →https://doi.org/10.1038/374183a0openalex-snapshot
A structural basis of the interactions between leucine-rich repeats and protein ligands
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Tubular membrane invaginations coated by dynamin rings are induced by GTP-γS in nerve terminals
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Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease.
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Ras/Rap effector specificity determined by charge reversal
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Mutations that affect the ability of the vnd/NK-2 homeoprotein to regulate gene expression: Transgenic alterations and tertiary structure
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Structure of an antibody-antigen complex: crystal structure of the HyHEL-10 Fab-lysozyme complex.
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Three-dimensional structure of a heteroclitic antigen-antibody cross-reaction complex.
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Recognition of specific DNA sequences by the c-myb protooncogene product: role of three repeat units in the DNA-binding domain.
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The single Cys2-His2 zinc finger domain of the GAGA protein flanked by basic residues is sufficient for high-affinity specific DNA binding.
inferredcites →https://doi.org/10.1073/pnas.96.3.811openalex-snapshot
Origins of DNA-binding specificity: Role of protein contacts with the DNA backbone
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Fasciculin 2 Binds to the Peripheral Site on Acetylcholinesterase and Inhibits Substrate Hydrolysis by Slowing a Step Involving Proton Transfer during Enzyme Acylation
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DNA Bending Is Essential for the Site-specific Recognition of DNA Response Elements by the DNA Binding Domain of the Tumor Suppressor Protein p53
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Equilibrium Binding of Estrogen Receptor with DNA Using Fluorescence Anisotropy
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Effect of Mutations at the Monomer-Monomer Interface of cAMP Receptor Protein on Specific DNA Binding
inferredcites →https://doi.org/10.1074/jbc.m004294200openalex-snapshot
DNA Binding Specificity Studies of Four ETS Proteins Support an Indirect Read-out Mechanism of Protein-DNA Recognition
inferredcites →https://doi.org/10.1093/bioinformatics/17.11.1027openalex-snapshot
Thermodynamic database for protein–nucleic acid interactions (ProNIT)
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PISCES: a protein sequence culling server
inferredcites →https://doi.org/10.1093/bioinformatics/btg243openalex-snapshot
Protein Ligand Database (PLD): additional understanding of the nature and specificity of protein–ligand complexes
inferredcites →https://doi.org/10.1093/nar/26.9.2143openalex-snapshot
DNA binding properties of a chemically synthesized DNA binding domain of hRFX1
inferredcites →https://doi.org/10.1093/nar/27.4.1063openalex-snapshot
The salt dependence of DNA recognition by NF-kappaB p50: a detailed kinetic analysis of the effects on affinityand specificity
inferredcites →https://doi.org/10.1093/nar/gkf495openalex-snapshot
Mutations altering the cleavage specificity of a homing endonuclease
inferredcites →https://doi.org/10.1093/nar/gkg389openalex-snapshot
The role of intercalating residues in chromosomal high-mobility-group protein DNA binding, bending and specificity
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Direct Fluorometric Determination of a Dissociation Constant as Low as 10−10 M for the Subtilisin BPN′-Protein Proteinase Inhibitor (Streptomyces Subtilisin Inhibitor) Complex by a Single Photon Counting Technique1
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Forces contributing to the conformational stability of proteins
inferredcites →https://doi.org/10.1110/ps.0211102openalex-snapshot
The role of helix stabilizing residues in GCN4 basic region folding and DNA binding
inferredcites →https://doi.org/10.1110/ps.0217002openalex-snapshot
Distance‐scaled, finite ideal‐gas reference state improves structure‐derived potentials of mean force for structure selection and stability prediction
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The Interaction of Bovine Pancreatic Deoxyribonuclease I and Skeletal Muscle Actin
inferredcites →https://doi.org/10.1126/science.1549776openalex-snapshot
Human Growth Hormone and Extracellular Domain of Its Receptor: Crystal Structure of the Complex
inferredcites →https://doi.org/10.1126/science.2451287openalex-snapshot
Reshaping Human Antibodies: Grafting an Antilysozyme Activity
inferredcites →https://doi.org/10.1126/science.274.5289.1001openalex-snapshot
Structure of the p53 Tumor Suppressor Bound to the Ankyrin and SH3 Domains of 53BP2
inferredcites →https://doi.org/10.1126/science.274.5289.1005openalex-snapshot
U1-Mediated Exon Definition Interactions Between AT-AC and GT-AG Introns
inferredcites →https://doi.org/10.1126/science.276.5311.431openalex-snapshot
Crystal Structure of the Nucleotide Exchange Factor GrpE Bound to the ATPase Domain of the Molecular Chaperone DnaK
inferredcites →https://doi.org/10.1126/science.3281254openalex-snapshot
Peroxisomal Membrane Ghosts in Zellweger Syndrome—Aberrant Organelle Assembly
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Inhibition of Porcine Glandular Kallikreins by Structurally Homologous Proteinase Inhibitors of the Kunitz (Trasylol) Type. Significance of the Basic Nature of Amino Acid Residues in Subside Positions for Kallikrein Inhibition
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The Dependence of All-Atom Statistical Potentials on Structural Training Database
inferredcites →https://doi.org/10.2174/0929867033457809openalex-snapshot
Ligand-Protein Docking: Cancer Research at the Interface between Biology and Chemistry
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Binding of the Recombinant Proteinase Inhibitor Eglin C from LeechHzrudo Medzcznalzsto Human Leukocyte Elastase, Bovine α-Chymotrypsin and Subtilisin Carlsberg: Thermodynamic Study
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The antigenic surface of staphylococcal nuclease. II. Analysis of the N-1 epitope by site-directed mutagenesis
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Exploration of Torsional Potential Energy Barrier and Electronic Origin of Torsional Flexibility of Common Flavonoids
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Docking and Scoring for Structure‐based Drug Design
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Modeling Protein‐Protein and Protein‐DNA Docking
inferred← citeshttps://doi.org/10.1002/9783527645947.ch10openalex-snapshot
Ligand and Receptor Conformational Energies
inferred← citeshttps://doi.org/10.1002/9783527645947.ch12openalex-snapshot
Scoring Functions for Protein–Ligand Interactions
inferred← citeshttps://doi.org/10.1002/9783527645947.ch15openalex-snapshot
Prospects of Modulating Protein–Protein Interactions
inferred← citeshttps://doi.org/10.1002/bab.2100openalex-snapshot
Integrative identification of human serpin PAI‐1 inhibitors from Dracaena dragon blood and molecular implications for inhibitor‐induced PAI‐1 allosterism
inferred← citeshttps://doi.org/10.1002/cem.3042openalex-snapshot
Genome‐wide feature analysis of the sequence‐specific recognition in intermolecular interaction between TGF‐β pathway DNA and MEG3 lncRNA in human cancer
inferred← citeshttps://doi.org/10.1002/jcc.20504openalex-snapshot
An iterative knowledge‐based scoring function to predict protein–ligand interactions: I. Derivation of interaction potentials
inferred← citeshttps://doi.org/10.1002/jcc.20505openalex-snapshot
An iterative knowledge‐based scoring function to predict protein–ligand interactions: II. Validation of the scoring function
inferred← citeshttps://doi.org/10.1002/jcc.20582openalex-snapshot
New computational strategy to analyze the interactions of ERα and ERβ with different ERE sequences
inferred← citeshttps://doi.org/10.1002/jcc.20756openalex-snapshot
Windock: Structure‐based drug discovery on windows‐based PCs
inferred← citeshttps://doi.org/10.1002/jcc.20924openalex-snapshot
Energy minimizations with a combination of two knowledge‐based potentials for protein folding
inferred← citeshttps://doi.org/10.1002/jcc.21078openalex-snapshot
A novel method for protein‐ligand binding affinity prediction and the related descriptors exploration
inferred← citeshttps://doi.org/10.1002/jcc.23170openalex-snapshot
Water PMF for predicting the properties of water molecules in protein binding site
inferred← citeshttps://doi.org/10.1002/jcc.23579openalex-snapshot
A Bayesian statistical approach of improving knowledge‐based scoring functions for protein–ligand interactions
inferred← citeshttps://doi.org/10.1002/jcc.23730openalex-snapshot
Carbohydrate-binding protein identification by coupling structural similarity searching with binding affinity prediction
inferred← citeshttps://doi.org/10.1002/minf.201300064openalex-snapshot
Development of QSAR‐Improved Statistical Potential for the Structure‐Based Analysis of ProteinPeptide Binding Affinities
inferred← citeshttps://doi.org/10.1002/minf.201500044openalex-snapshot
Streptococcus pneumoniae Genome‐wide Identification and Characterization of BOX Element‐binding Domains
inferred← citeshttps://doi.org/10.1002/pro.257openalex-snapshot
Quantitative prediction of protein–protein binding affinity with a potential of mean force considering volume correction
inferred← citeshttps://doi.org/10.1002/pro.580openalex-snapshot
A structure‐based benchmark for protein–protein binding affinity
inferred← citeshttps://doi.org/10.1002/prot.20512openalex-snapshot
Binding MOAD (Mother Of All Databases)
inferred← citeshttps://doi.org/10.1002/prot.20853openalex-snapshot
A correlation‐based method for the enhancement of scoring functions on funnel‐shaped energy landscapes
inferred← citeshttps://doi.org/10.1002/prot.21162openalex-snapshot
An all‐atom, distance‐dependent scoring function for the prediction of protein–DNA interactions from structure
inferred← citeshttps://doi.org/10.1002/prot.21310openalex-snapshot
A protein‐specifically adapted scoring function for the reranking of docking solutions
inferred← citeshttps://doi.org/10.1002/prot.21574openalex-snapshot
Predicting transmembrane helix pair configurations with knowledge‐based distance‐dependent pair potentials
inferred← citeshttps://doi.org/10.1002/prot.21674openalex-snapshot
Sampling of near‐native protein conformations during protein structure refinement using a coarse‐grained model, normal modes, and molecular dynamics simulations
inferred← citeshttps://doi.org/10.1002/prot.21844openalex-snapshot
A statistical rescoring scheme for protein–ligand docking: Consideration of entropic effect
inferred← citeshttps://doi.org/10.1002/prot.21867openalex-snapshot
Protein–protein docking by simulating the process of association subject to biochemical constraints
inferred← citeshttps://doi.org/10.1002/prot.21949openalex-snapshot
An iterative knowledge‐based scoring function for protein–protein recognition
inferred← citeshttps://doi.org/10.1002/prot.21968openalex-snapshot
Specific interactions for ab initio folding of protein terminal regions with secondary structures
inferred← citeshttps://doi.org/10.1002/prot.22189openalex-snapshot
Docking and scoring with alternative side‐chain conformations
inferred← citeshttps://doi.org/10.1002/prot.22323openalex-snapshot
A generalized knowledge‐based discriminatory function for biomolecular interactions
inferred← citeshttps://doi.org/10.1002/prot.22384openalex-snapshot
An all‐atom knowledge‐based energy function for protein‐DNA threading, docking decoy discrimination, and prediction of transcription‐factor binding profiles
inferred← citeshttps://doi.org/10.1002/prot.24564openalex-snapshot
Feature selection and classification of protein-protein complexes based on their binding affinities using machine learning approaches
inferred← citeshttps://doi.org/10.1002/prot.24607openalex-snapshot
Binding site multiplicity with fatty acid ligands: Implications for the regulation of PKR kinase autophosphorylation with palmitate
inferred← citeshttps://doi.org/10.1002/prot.24848openalex-snapshot
Optimizing the affinity and specificity of ligand binding with the inclusion of solvation effect
inferred← citeshttps://doi.org/10.1002/prot.25184openalex-snapshot
pyDock scoring for the new modeling challenges in docking: Protein–peptide, homo‐multimers, and domain–domain interactions
inferred← citeshttps://doi.org/10.1002/prot.25431openalex-snapshot
Continuous Automated Model EvaluatiOn (CAMEO) complementing the critical assessment of structure prediction in CASP12
inferred← citeshttps://doi.org/10.1002/prot.26821openalex-snapshot
PCANN Program for Structure‐Based Prediction of Protein–Protein Binding Affinity: Comparison With Other Neural‐Network Predictors
inferred← citeshttps://doi.org/10.1002/wcms.1410openalex-snapshot
Finding the ΔΔG spot: Are predictors of binding affinity changes upon mutations in protein–protein interactions ready for it?
inferred← citeshttps://doi.org/10.1002/wcms.1448openalex-snapshot
Computational prediction of protein–protein binding affinities
inferred← citeshttps://doi.org/10.1002/wcms.1571openalex-snapshot
RNA –ligand molecular docking: Advances and challenges
inferred← citeshttps://doi.org/10.1007/978-0-387-68372-0_3openalex-snapshot
Knowledge-Based Energy Functions for Computational Studies of Proteins
inferred← citeshttps://doi.org/10.1007/978-1-0716-3985-6_10openalex-snapshot
Assessment of Protein–Protein Docking Models Using Deep Learning
inferred← citeshttps://doi.org/10.1007/978-1-4419-6889-0_2openalex-snapshot
Multiscale Protein and Peptide Docking
inferred← citeshttps://doi.org/10.1007/978-1-4419-6889-0_6openalex-snapshot
Statistical Contact Potentials in Protein Coarse-Grained Modeling: From Pair to Multi-body Potentials
inferred← citeshttps://doi.org/10.1007/978-1-4939-6637-0_18openalex-snapshot
Probing Oligomerized Conformations of Defensin in the Membrane
inferred← citeshttps://doi.org/10.1007/978-3-319-63312-1_35openalex-snapshot
Protein-Protein Binding Affinity Prediction Based on Wavelet Package Transform and Two-Layer Support Vector Machines
inferred← citeshttps://doi.org/10.1007/978-3-642-14922-1_85openalex-snapshot
A Residual Level Potential of Mean Force Based Approach to Predict Protein-Protein Interaction Affinity
inferred← citeshttps://doi.org/10.1007/978-94-024-1069-3_8openalex-snapshot
Prediction of Biomolecular Complexes
inferred← citeshttps://doi.org/10.1007/978-981-16-1594-8_3openalex-snapshot
Energetic Aspects of Protein–Protein Interactions (PPIs)
inferred← citeshttps://doi.org/10.1007/s00214-010-0799-2openalex-snapshot
Trends in template/fragment-free protein structure prediction
inferred← citeshttps://doi.org/10.1007/s00214-017-2083-1openalex-snapshot
Feature functional theory–binding predictor (FFT–BP) for the blind prediction of binding free energies
inferred← citeshttps://doi.org/10.1007/s00726-011-1101-1openalex-snapshot
Structure-based prediction of protein–protein binding affinity with consideration of allosteric effect
inferred← citeshttps://doi.org/10.1007/s00894-012-1722-7openalex-snapshot
Structural and energetic insights into sequence-specific interaction in DNA–drug recognition: development of affinity predictor and analysis of binding selectivity
inferred← citeshttps://doi.org/10.1007/s10822-006-9047-1openalex-snapshot
A Virtual Active Compound Produced from the Negative Image of a Ligand-binding Pocket, and its Application to in-silico Drug Screening
inferred← citeshttps://doi.org/10.1007/s10822-012-9625-3openalex-snapshot
Biomacromolecular quantitative structure–activity relationship (BioQSAR): a proof-of-concept study on the modeling, prediction and interpretation of protein–protein binding affinity
inferred← citeshttps://doi.org/10.1007/s10822-014-9827-yopenalex-snapshot
A comparative study of family-specific protein–ligand complex affinity prediction based on random forest approach
inferred← citeshttps://doi.org/10.1007/s10822-016-9897-0openalex-snapshot
Incorporating specificity into optimization: evaluation of SPA using CSAR 2014 and CASF 2013 benchmarks
inferred← citeshttps://doi.org/10.1007/s10822-017-0042-5openalex-snapshot
Molden 2.0: quantum chemistry meets proteins
inferred← citeshttps://doi.org/10.1007/s10989-013-9354-zopenalex-snapshot
Structural and Affinity Insight into the Sequence-Specific Interaction of Transcription Factors DEC1 and DEC2 with E-box DNA: A Novel Model Peptide Approach
inferred← citeshttps://doi.org/10.1007/s12247-014-9202-5openalex-snapshot
Repurposing of Kinase Inhibitors to Target c-Abl as Potential Therapeutics for Alzheimer’s Disease
inferred← citeshttps://doi.org/10.1007/s12272-014-0495-1openalex-snapshot
Structure-based lead discovery for protein kinase C zeta inhibitor design by exploiting kinase–inhibitor complex crystal structure data and potential therapeutics for preterm labour
inferred← citeshttps://doi.org/10.1007/s12539-018-0304-5openalex-snapshot
Identification of Effective Dimeric Gramicidin-D Peptide as Antimicrobial Therapeutics over Drug Resistance: In-Silico Approach
inferred← citeshttps://doi.org/10.1007/s42250-026-01667-zopenalex-snapshot
Molecular Docking and Molecular Dynamic Simulations to Study the Interaction of HAA5 with Haloacid Dehalogenase from Pseudomonas Aeruginosa ITB1
inferred← citeshttps://doi.org/10.1016/b978-0-12-800168-4.00004-4openalex-snapshot
On the Use of Knowledge-Based Potentials for the Evaluation of Models of Protein–Protein, Protein–DNA, and Protein–RNA Interactions
inferred← citeshttps://doi.org/10.1016/b978-0-12-809633-8.20217-3openalex-snapshot
Protein-DNA Interactions
inferred← citeshttps://doi.org/10.1016/b978-0-323-90264-9.00024-6openalex-snapshot
Advances in structure-based virtual screening for drug discovery
inferred← citeshttps://doi.org/10.1016/b978-0-323-95502-7.00140-8openalex-snapshot
Emerging Topics in Protein-DNA Interactions
inferred← citeshttps://doi.org/10.1016/j.abb.2015.03.021openalex-snapshot
The cis conformation of proline leads to weaker binding of a p53 peptide to MDM2 compared to trans
inferred← citeshttps://doi.org/10.1016/j.ailsci.2023.100072openalex-snapshot
Bayesian optimization for ternary complex prediction (BOTCP)
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Amarogentin, a secoiridoid glycoside, activates AMP- activated protein kinase (AMPK) to exert beneficial vasculo-metabolic effects
inferred← citeshttps://doi.org/10.1016/j.bbamcr.2019.118612openalex-snapshot
Multiscale simulation unravel the kinetic mechanisms of inflammasome assembly
inferred← citeshttps://doi.org/10.1016/j.biomaterials.2022.121978openalex-snapshot
Chitosan and HPMCAS double-coating as protective systems for alginate microparticles loaded with Ctx(Ile21)-Ha antimicrobial peptide to prevent intestinal infections
inferred← citeshttps://doi.org/10.1016/j.bpc.2007.05.021openalex-snapshot
A novel empirical free energy function that explains and predicts protein–protein binding affinities
inferred← citeshttps://doi.org/10.1016/j.bpc.2009.05.003openalex-snapshot
Continued development of an empirical function for predicting and rationalizing protein–protein binding affinities
inferred← citeshttps://doi.org/10.1016/j.bpc.2022.106762openalex-snapshot
Importance of interface and surface areas in protein-protein binding affinity prediction: A machine learning analysis based on linear regression and artificial neural network
inferred← citeshttps://doi.org/10.1016/j.bpj.2021.11.016openalex-snapshot
rsRNASP: A residue-separation-based statistical potential for RNA 3D structure evaluation
inferred← citeshttps://doi.org/10.1016/j.chembiol.2011.01.005openalex-snapshot
Context-Based Identification of Protein-Protein Interfaces and “Hot-Spot” Residues
inferred← citeshttps://doi.org/10.1016/j.chemolab.2014.07.006openalex-snapshot
Prediction of protein–protein binding affinity using diverse protein–protein interface features
inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2015.01.001openalex-snapshot
Structure-based grafting and identification of kinase–inhibitors to target mTOR signaling pathway as potential therapeutics for glioblastoma
inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2015.12.003openalex-snapshot
Molecular design and structural optimization of potent peptide hydroxamate inhibitors to selectively target human ADAM metallopeptidase domain 17
inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2016.05.009openalex-snapshot
Systematic profiling of chemotherapeutic drug response to EGFR gatekeeper mutation in non-small cell lung cancer
inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2016.07.001openalex-snapshot
Revisiting the structural basis and energetic landscape of susceptibility difference between HLA isotypes to allergic rhinitis
inferred← citeshttps://doi.org/10.1016/j.compbiomed.2025.110438openalex-snapshot
Drug-target interaction/affinity prediction: Deep learning models and advances review
inferred← citeshttps://doi.org/10.1016/j.comptc.2012.04.010openalex-snapshot
Use of QM/MM scheme to reproduce macromolecule–small molecule noncovalent binding energy
inferred← citeshttps://doi.org/10.1016/j.csbj.2023.12.018openalex-snapshot
Systematic investigation of machine learning on limited data: A study on predicting protein-protein binding strength
inferred← citeshttps://doi.org/10.1016/j.drudis.2021.09.007openalex-snapshot
Machine-learning methods for ligand–protein molecular docking
inferred← citeshttps://doi.org/10.1016/j.ejmech.2006.12.028openalex-snapshot
In-silico drug screening method based on the protein–compound affinity matrix using the factor selection technique
inferred← citeshttps://doi.org/10.1016/j.febslet.2005.10.031openalex-snapshot
An all atom energy based computational protocol for predicting binding affinities of protein–ligand complexes
inferred← citeshttps://doi.org/10.1016/j.foodhyd.2025.111454openalex-snapshot
Alginate-pectin microparticles embedding self-assembling antimicrobial peptides and resveratrol for antimicrobial and anti-inflammatory applications
inferred← citeshttps://doi.org/10.1016/j.gene.2018.03.094openalex-snapshot
Identification of small-molecule ligands that bind to MiR-21 as potential therapeutics for endometriosis by screening ZINC database and in-vitro assays
inferred← citeshttps://doi.org/10.1016/j.gpb.2021.03.004openalex-snapshot
Computational Assessment of Protein–Protein Binding Affinity by Reversely Engineering the Energetics in Protein Complexes
inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2019.01.090openalex-snapshot
Heterologous expression and characterization of a new galactose-binding lectin from Bauhinia forficata with antiproliferative activity
inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2024.133811openalex-snapshot
A deep attention model for wide-genome protein-peptide binding affinity prediction at a sequence level
inferred← citeshttps://doi.org/10.1016/j.jmb.2005.11.036openalex-snapshot
Structure-based Prediction of bZIP Partnering Specificity
inferred← citeshttps://doi.org/10.1016/j.jmb.2017.12.001openalex-snapshot
e Repo-ORP: Exploring the Opportunity Space to Combat Orphan Diseases with Existing Drugs
inferred← citeshttps://doi.org/10.1016/j.jmgm.2005.11.006openalex-snapshot
Multiple target screening method for robust and accurate in silico ligand screening
inferred← citeshttps://doi.org/10.1016/j.jmgm.2006.02.010openalex-snapshot
A theory of mode of action of azolylalkylquinolines as DNA binding agents using automated flexible ligand docking
inferred← citeshttps://doi.org/10.1016/j.jmgm.2007.07.001openalex-snapshot
Prediction of protein–ligand complex structure by docking software guided by other complex structures
inferred← citeshttps://doi.org/10.1016/j.jmgm.2011.08.002openalex-snapshot
Protein–ligand docking guided by ligand pharmacophore-mapping experiment by NMR
inferred← citeshttps://doi.org/10.1016/j.jmgm.2014.07.010openalex-snapshot
An electronic environment and contact direction sensitive scoring function for predicting affinities of protein–ligand complexes in Contour®
inferred← citeshttps://doi.org/10.1016/j.jmgm.2021.107898openalex-snapshot
Scaffold-based analysis of nonpeptide oncogenic FTase inhibitors using multiple similarity matching, binding affinity scoring and enzyme inhibition assay
inferred← citeshttps://doi.org/10.1016/j.jtbi.2016.03.029openalex-snapshot
Discriminate protein decoys from native by using a scoring function based on ubiquitous Phi and Psi angles computed for all atom
inferred← citeshttps://doi.org/10.1016/j.molp.2018.10.010openalex-snapshot
Building Transcription Factor Binding Site Models to Understand Gene Regulation in Plants
inferred← citeshttps://doi.org/10.1016/j.sbi.2020.05.017openalex-snapshot
Computational structure modeling for diverse categories of macromolecular interactions
inferred← citeshttps://doi.org/10.1016/j.ymeth.2014.10.019openalex-snapshot
Structure based virtual screening to discover putative drug candidates: Necessary considerations and successful case studies
inferred← citeshttps://doi.org/10.1016/s0065-3233(05)72001-5openalex-snapshot
Potential Functions for Hydrogen Bonds in Protein Structure Prediction and Design
inferred← citeshttps://doi.org/10.1016/s1574-1400(10)06014-7openalex-snapshot
Mean-Force Scoring Functions for Protein–Ligand Binding
inferred← citeshttps://doi.org/10.1021/acs.biochem.5c00622openalex-snapshot
Sweet Protein Allosteric Binding and Activation of the Human T1R2/R3 Sweet Receptor: A Simulation Model Validated by in Vitro Receptor Activation Assay
inferred← citeshttps://doi.org/10.1021/acs.chemrev.3c00550openalex-snapshot
Computational Approaches to Predict Protein–Protein Interactions in Crowded Cellular Environments
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00203openalex-snapshot
AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings
inferred← citeshttps://doi.org/10.1021/acs.jcim.4c01850openalex-snapshot
ProAffinity-GNN: A Novel Approach to Structure-Based Protein–Protein Binding Affinity Prediction via a Curated Data Set and Graph Neural Networks
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00372openalex-snapshot
Knowledge of Native Protein–Protein Interfaces Is Sufficient To Construct Predictive Models for the Selection of Binding Candidates
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c00427openalex-snapshot
Improved Prediction of Drug–Protein Interactions through Physics-Based Few-Shot Learning
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00677openalex-snapshot
TetraBASE: A Side Chain-Independent Statistical Energy for Designing Realistically Packed Protein Backbones
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00619openalex-snapshot
Prediction of the Favorable Hydration Sites in a Protein Binding Pocket and Its Application to Scoring Function Formulation
inferred← citeshttps://doi.org/10.1021/acs.jctc.8b00516openalex-snapshot
Generation of Pairwise Potentials Using Multidimensional Data Mining
inferred← citeshttps://doi.org/10.1021/acs.jproteome.1c00612openalex-snapshot
EXCESP: A Structure-Based Online Database for Extracellular Interactome of Cell Surface Proteins in Humans
inferred← citeshttps://doi.org/10.1021/acsomega.3c06996openalex-snapshot
Predictive Models and Impact of Interfacial Contacts and Amino Acids on Protein–Protein Binding Affinity
inferred← citeshttps://doi.org/10.1021/bi700065hopenalex-snapshot
Purification and Characterization of the FeII- and α-Ketoglutarate-Dependent Xanthine Hydroxylase from Aspergillus nidulans
inferred← citeshttps://doi.org/10.1021/ci100343jopenalex-snapshot
Knowledge-Based Scoring Functions in Drug Design: 2. Can the Knowledge Base Be Enriched?
inferred← citeshttps://doi.org/10.1021/ci100473dopenalex-snapshot
Global Free Energy Scoring Functions Based on Distance-Dependent Atom-Type Pair Descriptors
inferred← citeshttps://doi.org/10.1021/ci100490wopenalex-snapshot
Target-Specific Support Vector Machine Scoring in Structure-Based Virtual Screening: Computational Validation, In Vitro Testing in Kinases, and Effects on Lung Cancer Cell Proliferation
inferred← citeshttps://doi.org/10.1021/ci2000665openalex-snapshot
Ligand Identification Scoring Algorithm (LISA)
inferred← citeshttps://doi.org/10.1021/ci2000727openalex-snapshot
Scoring and Lessons Learned with the CSAR Benchmark Using an Improved Iterative Knowledge-Based Scoring Function
inferred← citeshttps://doi.org/10.1021/ci200078fopenalex-snapshot
Support Vector Regression Scoring of Receptor–Ligand Complexes for Rank-Ordering and Virtual Screening of Chemical Libraries
inferred← citeshttps://doi.org/10.1021/ci200193zopenalex-snapshot
AADS- An Automated Active Site Identification, Docking, and Scoring Protocol for Protein Targets Based on Physicochemical Descriptors
inferred← citeshttps://doi.org/10.1021/ci200274qopenalex-snapshot
DSX: A Knowledge-Based Scoring Function for the Assessment of Protein–Ligand Complexes
inferred← citeshttps://doi.org/10.1021/ci300377fopenalex-snapshot
Comprehensive Classification and Diversity Assessment of Atomic Contacts in Protein–Small Ligand Interactions
inferred← citeshttps://doi.org/10.1021/ci300619xopenalex-snapshot
Development of the Knowledge-Based and Empirical Combined Scoring Algorithm (KECSA) To Score Protein–Ligand Interactions
inferred← citeshttps://doi.org/10.1021/ci400045vopenalex-snapshot
Automated Large-Scale File Preparation, Docking, and Scoring: Evaluation of ITScore and STScore Using the 2012 Community Structure–Activity Resource Benchmark
inferred← citeshttps://doi.org/10.1021/ci400302dopenalex-snapshot
HotLig: A Molecular Surface-Directed Approach to Scoring Protein–Ligand Interactions
inferred← citeshttps://doi.org/10.1021/ci400510eopenalex-snapshot
Nonlinear Scoring Functions for Similarity-Based Ligand Docking and Binding Affinity Prediction
inferred← citeshttps://doi.org/10.1021/ci7004719openalex-snapshot
An Improved PMF Scoring Function for Universally Predicting the Interactions of a Ligand with Protein, DNA, and RNA
inferred← citeshttps://doi.org/10.1021/ci800435xopenalex-snapshot
In Silico Fragment Screening by Replica Generation (FSRG) Method for Fragment-Based Drug Design
inferred← citeshttps://doi.org/10.1021/ci9000053openalex-snapshot
Comparative Assessment of Scoring Functions on a Diverse Test Set
inferred← citeshttps://doi.org/10.1021/ci9002156openalex-snapshot
Protein−Ligand Binding Free Energy Calculation by the Smooth Reaction Path Generation (SRPG) Method
inferred← citeshttps://doi.org/10.1021/ci9002987openalex-snapshot
Inclusion of Solvation and Entropy in the Knowledge-Based Scoring Function for Protein−Ligand Interactions
inferred← citeshttps://doi.org/10.1021/ct400295zopenalex-snapshot
Intermolecular Contact Potentials for Protein–Protein Interactions Extracted from Binding Free Energy Changes upon Mutation
inferred← citeshttps://doi.org/10.1021/ct600195fopenalex-snapshot
Assessment of Detection and Refinement Strategies for de novo Protein Structures Using Force Field and Statistical Potentials
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/jm8016464openalex-snapshot
Structural Artifacts in Protein−Ligand X-ray Structures: Implications for the Development of Docking Scoring Functions
inferred← citeshttps://doi.org/10.1021/pr9009854openalex-snapshot
Are Scoring Functions in Protein−Protein Docking Ready To Predict Interactomes? Clues from a Novel Binding Affinity Benchmark
inferred← citeshttps://doi.org/10.1038/s41401-025-01659-8openalex-snapshot
Harnessing deep statistical potential for biophysical scoring of protein-peptide interactions
inferred← citeshttps://doi.org/10.1038/s41467-025-59987-6openalex-snapshot
High-speed atomic force microscopy and 3D modeling reveal the structural dynamics of ADAR1 complexes
inferred← citeshttps://doi.org/10.1038/s41540-018-0050-7openalex-snapshot
Large-scale computational drug repositioning to find treatments for rare diseases
inferred← citeshttps://doi.org/10.1038/s41598-020-57778-1openalex-snapshot
PreDBA: A heterogeneous ensemble approach for predicting protein-DNA binding affinity
inferred← citeshttps://doi.org/10.1038/s41598-024-81287-0openalex-snapshot
The potential inhibitory mechanism of EGCG against the Chikungunya virus targeting non-structural protein 2 through molecular dynamics simulation
inferred← citeshttps://doi.org/10.1038/s43588-022-00389-9openalex-snapshot
Binding affinity estimation from restrained umbrella sampling simulations
inferred← citeshttps://doi.org/10.1039/9781849735377-00195openalex-snapshot
Binding Free Energy Calculation and Scoring in Small-Molecule Docking
inferred← citeshttps://doi.org/10.1039/b821580dopenalex-snapshot
Fast predictions of thermodynamics and kinetics of protein–protein recognition from structures: from molecular design to systems biology
inferred← citeshttps://doi.org/10.1039/c0cp00151aopenalex-snapshot
Scoring functions and their evaluation methods for protein–ligand docking: recent advances and future directions
inferred← citeshttps://doi.org/10.1039/c4qi00018hopenalex-snapshot
Study of single and double chain surfactant–cobalt( iii ) complexes and their hydrophobicity, micelle formation, interaction with serum albumins and antibacterial activities
inferred← citeshttps://doi.org/10.1049/iet-syb.2014.0066openalex-snapshot
Knowledge‐based three‐body potential for transcription factor binding site prediction
inferred← citeshttps://doi.org/10.1063/1.5027243openalex-snapshot
Improving low-accuracy protein structures using enhanced sampling techniques
inferred← citeshttps://doi.org/10.1063/1.5133601openalex-snapshot
Survey of the scoring functions for protein-ligand docking
inferred← citeshttps://doi.org/10.1073/pnas.2000585117openalex-snapshot
Machine learning classification can reduce false positives in structure-based virtual screening
inferred← citeshttps://doi.org/10.1074/jbc.m506342200openalex-snapshot
A Conserved Glutamate Residue in Transmembrane Helix 10 Influences Substrate Specificity of Rabbit OCT2 (SLC22A2)
inferred← citeshttps://doi.org/10.1074/jbc.m603810200openalex-snapshot
The Unorthodox SNAP50 Zinc Finger Domain Contributes to Cooperative Promoter Recognition by Human SNAPC
inferred← citeshttps://doi.org/10.1080/07391102.2017.1334596openalex-snapshot
In silico identification of potential drug compound against Peroxisome proliferator-activated receptor-gamma by virtual screening and toxicity studies for the treatment of Diabetic Nephropathy
inferred← citeshttps://doi.org/10.1080/07391102.2020.1736158openalex-snapshot
Screening and molecular characterization of lethal mutations of human homogentisate 1, 2 dioxigenase
inferred← citeshttps://doi.org/10.1080/10409238.2017.1380596openalex-snapshot
Finding the needle in the haystack: towards solving the protein-folding problem computationally
inferred← citeshttps://doi.org/10.1080/1062936x.2017.1292406openalex-snapshot
Structure-based modelling, scoring, screening, andin vitrokinase assay of anesthetic pkc inhibitors against a natural medicine library
inferred← citeshttps://doi.org/10.1080/14786419.2014.955491openalex-snapshot
Virtual screening of protein kinase C inhibitors from natural product library to modulate general anaesthetic effects
inferred← citeshttps://doi.org/10.1088/1674-1056/abc0d6openalex-snapshot
Statistical potentials for 3D structure evaluation: From proteins to RNAs*
inferred← citeshttps://doi.org/10.1088/2399-6528/abea27openalex-snapshot
Binding of SARS-CoV-2/SARS-CoV spike protein with human ACE2 receptor
inferred← citeshttps://doi.org/10.1088/2632-2153/ae29bcopenalex-snapshot
CAP: Commutative algebra prediction of protein-nucleic acid binding affinities
inferred← citeshttps://doi.org/10.1089/cmb.2019.0251openalex-snapshot
All-Atom Knowledge-Based Potential for RNA Structure Discrimination Based on the Distance-Scaled Finite Ideal-Gas Reference State
inferred← citeshttps://doi.org/10.1093/bib/bbac097openalex-snapshot
Integrated unsupervised–supervised modeling and prediction of protein–peptide affinities at structural level
inferred← citeshttps://doi.org/10.1093/bib/bbad192openalex-snapshot
emPDBA: protein-DNA binding affinity prediction by combining features from binding partners and interface learned with ensemble regression model
inferred← citeshttps://doi.org/10.1093/bioinformatics/btl275openalex-snapshot
Intramolecular surface contacts contain information about protein–protein interface regions
inferred← citeshttps://doi.org/10.1093/bioinformatics/btq295openalex-snapshot
Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function
inferred← citeshttps://doi.org/10.1093/bioinformatics/btr513openalex-snapshot
Protein–protein binding affinity prediction on a diverse set of structures
inferred← citeshttps://doi.org/10.1093/bioinformatics/bts699openalex-snapshot
A knowledge-based orientation potential for transcription factor-DNA docking
inferred← citeshttps://doi.org/10.1093/bioinformatics/btt121openalex-snapshot
Specificity and affinity quantification of protein–protein interactions
inferred← citeshttps://doi.org/10.1093/bioinformatics/btu104openalex-snapshot
Improved protein–ligand binding affinity prediction by using a curvature-dependent surface-area model
inferred← citeshttps://doi.org/10.1093/bioinformatics/btu580openalex-snapshot
Protein–protein binding affinity prediction from amino acid sequence
inferred← citeshttps://doi.org/10.1093/bioinformatics/btw264openalex-snapshot
Structure-based prediction of transcription factor binding specificity using an integrative energy function
inferred← citeshttps://doi.org/10.1093/bioinformatics/btx698openalex-snapshot
Predicting protein–DNA binding free energy change upon missense mutations using modified MM/PBSA approach: SAMPDI webserver
inferred← citeshttps://doi.org/10.1093/bioinformatics/btz544openalex-snapshot
Artificial intelligence-based multi-objective optimization protocol for protein structure refinement
inferred← citeshttps://doi.org/10.1093/gigascience/giy091openalex-snapshot
eModel-BDB: a database of comparative structure models of drug-target interactions from the Binding Database
inferred← citeshttps://doi.org/10.1093/nar/gki360openalex-snapshot
Web-based toolkits for topology prediction of transmembrane helical proteins, fold recognition, structure and binding scoring, folding-kinetics analysis and comparative analysis of domain combinations
inferred← citeshttps://doi.org/10.1093/nar/gkl1103openalex-snapshot
Energetics of protein–DNA interactions
inferred← citeshttps://doi.org/10.1093/nar/gkl1155openalex-snapshot
Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry
inferred← citeshttps://doi.org/10.1093/nar/gkp289openalex-snapshot
Experimentally based contact energies decode interactions responsible for protein–DNA affinity and the role of molecular waters at the binding interface
inferred← citeshttps://doi.org/10.1093/nar/gkp852openalex-snapshot
BioDrugScreen: a computational drug design resource for ranking molecules docked to the human proteome
inferred← citeshttps://doi.org/10.1093/nar/gkq1266openalex-snapshot
Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets
inferred← citeshttps://doi.org/10.1093/nar/gkr531openalex-snapshot
Towards computional specificity screening of DNA-binding proteins
inferred← citeshttps://doi.org/10.1093/nar/gks564openalex-snapshot
DBD2BS: connecting a DNA-binding protein with its binding sites
inferred← citeshttps://doi.org/10.1093/nar/gkv493openalex-snapshot
NPDock: a web server for protein–nucleic acid docking
inferred← citeshttps://doi.org/10.1093/nar/gkx255openalex-snapshot
SPA-LN: a scoring function of ligand–nucleic acid interactions via optimizing both specificity and affinity
inferred← citeshttps://doi.org/10.1093/plphys/kiaf392openalex-snapshot
The N-terminal domain of COMPANION OF CELLULOSE SYNTHASE1 promotes microtubule array formation in Arabidopsis
inferred← citeshttps://doi.org/10.1098/rsif.2012.0835openalex-snapshot
On the binding affinity of macromolecular interactions: daring to ask why proteins interact
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