A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules J. Am. Chem. Soc. 1995, 117, 5179−5197

No abstract is available for this paper.

• Publication year

  1996

• Venue

  Journal of the American Chemical Society

• Publication date

  1996-03-06

• Fields of study

  Chemistry

• Identifiers
  DOI 10.1021/JA955032E
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

• No references are available for this paper.

• SITH: A Quantum-Chemical Framework for Predicting Bond Destabilization in Stretched Molecules

  2026cites this paper
• Structural barriers of the discrete Hasimoto map applied to protein backbone geometry

  2026cites this paper
• Exploring Conformational Transitions of RNA Dimers via Machine Learning Potentials

  2026cites this paper
• Computational dual-loop frameworks bridging single-enzyme design and cascade tunnel network engineering for next-generation biosynthetic systems.

  2026cites this paper
• Enhancing interfacial adhesion of chitosan coatings on waxy fruit cuticles via a calcium-gallic acid metal-phenolic network

  2026cites this paper
• Driving Catalytic Innovation: The Development and Application of Machine Learning Force Fields

  2026cites this paper
• Scalable Force Fields for Metal-Mediated DNA Nanostructures.

  2026cites this paper
• A full in-silico approach for quantifying the effect of intramolecular hydrogen bonds on physicochemical properties

  2025cites this paper
• A Nonlocal size modified Poisson-Boltzmann Model and Its Finite Element Solver for Protein in Multi-Species Ionic Solution

  2025cites this paper
• Decoding Hairpin Structure Stability in Lin28-Mediated Repression.

  2025cites this paper
• Highly Brominated Quinolines: Synthesis, Characterization, and Investigation of Anticancer Activities Supported by Molecular Dynamics

  2025cites this paper
• Water-directed pinning is key to tau prion formation

  2025cites this paper
• Symmetry-Driven Discovery of Dynamical Variables in Molecular Simulations

  2025influential citation
• Predicting 3D Structures of Lasso Peptides

  2025cites this paper
• Computational investigation of uracil dimers in water and the role of classical potentials.

  2025cites this paper
• Lightweight MSA Design Advances Protein Folding From Evolutionary Embeddings

  2025cites this paper
• Confined static microstructures and dynamics of glycerol molecules within sub-2-nm diameter carbon nanotubes: Molecular dynamics study

  2025cites this paper
• Loop Dynamics Perturbation Enhances the Catalytic Stability of GH18 Family Chitinases.

  2025cites this paper
• Structural basis of bis-quinolinium ligands binding to quadruplex–duplex hybrids from PIM1 oncogene

  2025cites this paper
• FINCHES: A Computational Framework for Predicting Intermolecular Interactions in Intrinsically Disordered Proteins

  2025cites this paper
• RNA G-quadruplexes emerge from a compacted coil-like ensemble via multiple pathways

  2025influential citation
• Nano-Zeolite-Encapsulated Amentoflavone: A Computationally Designed and Experimentally Validated Anti-SARS-CoV-2 Therapeutic

  2025cites this paper
• The Kink-Turn 7 Motif: An Additional Test for RNA Force Field Performance

  2025cites this paper
• Automated Workflow for Absolute Binding Free Energy Calculations with Implicit Solvent and Double Decoupling

  2025cites this paper
• When does molecular dynamics improve RNA models? Insights from CASP15 and practical guidelines

  2025cites this paper
• Structure‐Guided Engineering of a Versatile Urethanase Improves Its Polyurethane Depolymerization Activity

  2025cites this paper
• Unknotting RNA: A method to resolve computational artifacts

  2025cites this paper
• Deciphering Mn2+ Solvation and Interfacial Chemistry for Rechargeable Nonaqueous Mn-Metal Batteries.

  2025cites this paper
• Anomalous double-layer restructuring in water-in-salt electrolytes at graphitic interfaces governs capacitance

  2025cites this paper
• MLIPAudit: A benchmarking tool for Machine Learned Interatomic Potentials

  2025cites this paper
• Impact of Solvents on the Crystal Morphology of CL-20/TFAZ Cocrystals: A Predictive Study

  2025cites this paper
• Role of Individual Amino Acid Residues Directly Involved in Damage Recognition in Active Demethylation by ABH2 Dioxygenase

  2025influential citation
• Theoretical Investigation of the Functional Divergence of StnK3 via Site-Directed Mutagenesis: From Epimerase to Retro-Aldolase.

  2025cites this paper
• Illuminating Protein Dynamics: A Review of Computational Methods for Studying Photoactive Proteins

  2025cites this paper
• Atomic-Level Understanding of Contact Potential of Quartz Surface

  2025cites this paper
• Rare but specific: 5-bp composite motifs define SMAD binding in BMP signaling

  2025cites this paper
• Non-equilibrium molecular simulations reveal a pore-flow-dominated transport mechanism in pervaporation membranes

  2025cites this paper
• Boltz-ABFE: Free Energy Perturbation without Crystal Structures.

  2025cites this paper
• Coarse‐Grained DNA Models: Bridging Scales Through Extended Dynamics

  2025cites this paper
• Hydrogen Bond-Induced Binding between Organofluorine and Protein via Fluorine Atoms: A Database Survey and Quantum Chemistry Calculation Study.

  2025cites this paper
• Current Advances in Genome Modeling Across Length Scales

  2025cites this paper
• Graphene functionalized with 2–mercaptobenzimidazole derivatives: Structural and bonding analysis on metal cation adsorption in water

  2025cites this paper
• Nobiletin protected against hypertrophic cardiomyopathy via targeting PPARα

  2025cites this paper
• Structural and Helix Reversal Defects of Carbon Nanosprings: A Molecular Dynamics Study

  2025cites this paper
• Characterization of Protein-Ligand Chalcogen Bonds: Insights from Database Survey and Quantum Mechanics Calculations

  2025cites this paper
• Advanced Investigation of Pentagalloylglucose Nano-Zeolite Formulation as a Potent Inhibitor of SARS-CoV-2 3 CLpro: A Synergistic Integration of Computational Modelling and Experimental Validation

  2025cites this paper
• How Do Transport Mechanisms Shape Material Design in RO Membranes? A Molecular Dynamics Perspective

  2025cites this paper
• Orally delivered toxin–binding protein protects against diarrhoea in a murine cholera model

  2025cites this paper
• Advancements in Computer-Aided Drug Design: A Comprehensive Review

  2025cites this paper
• Molecular interaction study of flavonols with human serum albumin by theoretical simulations.

  2025cites this paper
• Identification and inhibition of PIN1-NRF2 protein–protein interactions through computational and biophysical approaches

  2025cites this paper
• Machine learning surrogate models of many-body dispersion interactions in polymer melts

  2025cites this paper
• Identification of a serine protease involved in spinosad degradation in the yellow fever mosquito, Aedes aegypti

  2025cites this paper
• Microscopic insights on CO2/N2 separation in functionalized MOFs from molecular dynamics simulations and density functional theory calculation

  2025cites this paper
• Evidence for the Progressive Improvement of All-Atom Force Fields in Reproducing Local Conformational Preferences of Flexible Peptides

  2025cites this paper
• Machine learning approaches for interpretable antibody property prediction using structural data

  2025cites this paper
• PLAME: Leveraging Pretrained Language Models to Generate Enhanced Protein Multiple Sequence Alignments

  2025cites this paper
• N-[(Thiophen-3-yl)methyl]benzamides as Influenza Virus Fusion Inhibitors Acting on H1 and H5 Hemagglutinins

  2025cites this paper
• Microscopic Exploration of Water Permeation and Ion Rejection for Edge Amine-Functionalized GO Nanoslits

  2025cites this paper
• Revisiting Fluorobenzene as Diluents in Ether-Based Electrolytes for Lithium Metal Batteries

  2025cites this paper
• The energy landscape of N-ribosidic bond cleavage catalysed by 2′-deoxynucleoside 5′-phosphate N-hydrolase 1

  2025cites this paper
• Martini Mapper: An Automated Fragment-Based Framework for Developing Coarse-Grained Models within the Martini 3 Framework

  2025cites this paper
• Integrated NMR and MD structure and dynamics of the stem–loop-II motif (s2m) from the Omicron variant of SARS-CoV-2

  2025influential citation
• Methodological Approach Based on Structural Parameters, Vibrational Frequencies, and MMFF94 Bond Charge Increments for Platinum-Based Compounds

  2025cites this paper
• Quantum Encoding of Three-Dimensional Ligand Poses for Exhaustive Configuration Enumeration

  2025cites this paper
• Chemical Inhibition of Splicing-Related Protein Kinases Reveals Phosphorylation-Driven Regulation of RNA Alternative Splicing in Arabidopsis Seedlings

  2025cites this paper
• Uncovering the Role of Distal Regions in PDK1 Allosteric Activation

  2025cites this paper
• Quantum algorithm for Ewald summation based computation of long-range electrostatics

  2025cites this paper
• Chemical Identification of [Fe(III)(OH)(H2O)]2+ Complex Ion at the Ferroxidase Active Site in Cryo-EM Maps.

  2025cites this paper
• Attenuating ETEC virulence using a heat-labile enterotoxin–blocking binding protein

  2025cites this paper
• AlphaNet: Scaling Up Local-frame-based Atomistic Interatomic Potential

  2025cites this paper
• Nonequilibrium dynamics of the helix-coil transition in polyalanine.

  2025cites this paper
• Enhanced Bioactivity of Natural Products by Halogenation: A Database Survey and Quantum Chemistry Calculation Study.

  2025cites this paper
• Ensemble Learning of Machine Learning Force Fields

  2024cites this paper
• A hemoprotein with a zinc-mirror heme site ties heme availability to carbon metabolism in cyanobacteria

  2024cites this paper
• Impact of Halogen Bonds on Protein-Peptide Binding and Protein Structural Stability Revealed by Computational Approaches.

  2024cites this paper
• Graph Fourier Neural ODEs: Modeling Spatial-temporal Multi-scales in Molecular Dynamics

  2024cites this paper
• Resonant multiphoton processes and excitation limits to structural dynamics

  2024cites this paper
• Stability-Aware Training of Machine Learning Force Fields with Differentiable Boltzmann Estimators

  2024cites this paper
• Adsorption and Diffusion Properties of Functionalized MOFs for CO2 Capture: A Combination of Molecular Dynamics Simulation and Density Functional Theory Calculation.

  2024cites this paper
• AI-augmented physics-based docking for antibody-antigen complex prediction

  2024cites this paper
• Biological Implications of the Intrinsic Deformability of Human Acetylcholinesterase Induced by Diverse Compounds: A Computational Study

  2024cites this paper
• Hydration Waters Make Up for the Missing Third Hydrogen Bond in the A·T Base Pair

  2024cites this paper
• Parameterization of General Organic Polymers within the Open Force Field Framework

  2024cites this paper
• Electrical property-selective noncovalent dispersion of carbon nanotubes by poly(perylene diimide-thiophene): a molecular dynamics study

  2024influential citation
• Deep learning path-like collective variable for enhanced sampling molecular dynamics.

  2024cites this paper
• Can We Ever Develop an Ideal RNA Force Field? Lessons Learned from Simulations of the UUCG RNA Tetraloop and Other Systems

  2024cites this paper
• Metal Ion Sensing by Tetraloop-Like RNA Fragment: Role of Compact Intermediates with Non-Native Metal Ion-RNA Inner Shell Contacts

  2024cites this paper
• Molecular simulations of increased thermal energy storage in metal–organic heat carriers with R1234ze(E)/R32 mixtures combined with IRMOF-1

  2024cites this paper
• MDRefine: A Python package for refining molecular dynamics trajectories with experimental data.

  2024cites this paper
• Impact of water models on structure and dynamics of enzyme tunnels

  2024cites this paper
• Getting the intermolecular forces correct: introducing the ASTA strategy for a water model

  2024cites this paper
• Invariant dynamics in a united-atom model of an ionic liquid.

  2024cites this paper
• Development of a Fluctuating Charge Model for Zinc-Containing Metalloproteins

  2024cites this paper
• RBMD: A Molecular Dynamics Package Enabling to Simulate 10 Million All-Atom Particles in a Single Graphics Processing Unit

  2024cites this paper
• Self-assembly of mycolic acid in water: monolayer or bilayer

  2024cites this paper
• Physical insights into the molecular mechanisms governing structural and dynamic properties of choline chloride-based deep eutectic solvents

  2024cites this paper
• Molecular dynamics simulation in tissue engineering

  2024cites this paper
• DEVELOPMENT OF APPROACHES TO MOLECULAR MODELING OF THE INTERACTION OF BIOLOGICALLY ACTIVE COMPONENTS OF HUMIC SUBSTANCES WITH BETA-LACTAMASES ON THE EXAMPLE OF HUMIC-LIKE LOW-MOLECULAR WEIGHT ANALOGUES

  2024cites this paper
• Improving Antibody Design with Force-Guided Sampling in Diffusion Models

  2024cites this paper