Improvements to the APBS biomolecular solvation software suite

2017/08/24 by Elizabeth Jurrus, Dave Engel, Keith T. Star +28 · 32 citations
Biochemistry, Genetics and Molecular Biology · #Advanced Fluorescence Microscopy Techniques #Gene Regulatory Network Analysis #Protein Structure and Dynamics

paper · pdf · doi:10.1002/pro.3280

openalex created_date 2017/07/14 · openalex publication_date 2017/08/24 · openalex updated_date 2026/07/31

Abstract

Abstract The Adaptive Poisson–Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that have provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses the three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this article, we discuss the models and capabilities that have recently been implemented within the APBS software package including a Poisson–Boltzmann analytical and a semi‐analytical solver, an optimized boundary element solver, a geometry‐based geometric flow solvation model, a graph theory‐based algorithm for determining p K a values, and an improved web‐based visualization tool for viewing electrostatics.

Citations

• Jaguar: A high‐performance quantum chemistry software program with strengths in life and materials sciences
• Very fast empirical prediction and rationalization of protein pKa values

Cited by

• Analysis of the heterogenous structural states of the hexameric ATPase PilU of the type IV pili from Vibrio cholerae
• Architecture of the 8 MDa Hdr–Vhu–Fwd super-assembly in class I methanogens
• AcuB senses cellular energy charge to coordinate acetyl-CoA synthesis in bacteria
• Assessing the validity of leucine zipper constructs predicted by AlphaFold
• Ancestral Chaperonins Provide the First Structural Glimpse into Early Multimeric Protein Evolution
• COMPOSITUM 2 / WHEAT FRIZZY PANICLE dosage dependently regulates inflorescence and root architecture in Triticeae cereals
• Dual E3 ligase recruitment by monovalent degraders for tunable SMARCA 2/4 degradation
• Predicting protein variant properties with electrostatic representations
• Functional and structural characterization of Stenotrophomonas maltophilia EntB, an unusual form of isochorismatase for siderophore synthesis
• Exploring Use of a Protein Cage System for Producing Bioactive Peptides in Escherichia coli
• Crystal structure of dihydroorotate dehydrogenase from Helicobacter pylori with bound flavin mononucleotide
• Inhibition mechanism of potential antituberculosis compound lansoprazole sulfide
• Engineered Protein‐Based Ionic Conductors for Sustainable Energy Storage Applications
• Sensitive red fluorescent indicators for real-time visualization of potassium ion dynamics in vivo
• SHREC 2025: Protein surface shape retrieval including electrostatic potential
• From Binding to Catalysis: Emergence of a Rudimentary Enzyme Conferring Intrinsic Antibiotic Resistance
• Computational modeling of biological nanopores
• gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS
• Molecular Basis for Short-Chain Thioester Hydrolysis by Acyl Hydrolases in trans-Acyltransferase Polyketide Synthases
• Virus adaptation to heparan sulfate comes with capsid stability tradeoff
• Engineering surface electrostatics affords control over morphological preference, synergy, and activity in polymer degrading enzymes
• Plant polygalacturonase structures specify enzyme dynamics and processivities to fine-tune cell wall pectins
• An Integral Equation Formulation of the N-body Dielectric Spheres\n Problem. Part II: Complexity Analysis
• A high-resolution data set of fatty acid-binding protein structures. I. Dynamics of FABP4 and ligand binding
• Structural Bases of Dihydroxy Acid Dehydratase Inhibition and Biodesign for Self-Resistance
• Transfer Learning for Protein Structure Classification at Low Resolution
• Structural Factors and Electron Transfer Mechanisms in Flavoenzymes
• Shikimate Kinase-Like 1 Participates in an Ancient and Conserved Role Contributing to Chloroplast Biogenesis in Land Plants
• Charge engineering controls cooperative assembly and loading in protein host–guest complexes
• Structural basis for OAS2 regulation and its antiviral function
• Structure and unusual binding mechanism of the hyaluronan receptor LYVE-1 mediating leucocyte entry to lymphatics
• Acquired Immune Deficiency Syndrome correlation with SARS-CoV-2 N genotypes

Related

• NextGenPB: an analytically-enabled super resolution and local (de)refinement Poisson-Boltzmann Equation solver
• Poisson-Boltzmann based machine learning (PBML) model for electrostatic analysis
• Accurate, robust and reliable calculations of Poisson-Boltzmann solvation energies
• PB-AM: An Open-Source, Fully Analytical Linear Poisson-Boltzmann Solver
• Coupling finite and boundary element methods to solve the Poisson--Boltzmann equation for electrostatics in molecular solvation