Integration in a depot‐based decentralized biorefinery system: Corn stover‐based cellulosic biofuel

The current or “conventional” paradigm for producing process energy in a biorefinery processing cellulosic biomass is on‐site energy recovery through combustion of residual solids and biogas generated by the process. Excess electricity is then exported, resulting in large greenhouse gas (GHG) credits. However, this approach will cause lifecycle GHG emissions of biofuels to increase as more renewable energy sources (wind, solar, etc.) participate in grid‐electricity generation, and the GHG credits from displacing fossil fuel decrease. To overcome this drawback, a decentralized (depot‐based) biorefinery can be integrated with a coal‐fired power plant near a large urban area. In an integrated, decentralized, depot‐based biorefinery (IDB), the residual solids are co‐fired with coal either in the adjacent power plant or in coal‐fired boilers elsewhere to displace coal. An IDB system does not rely on indirect GHG credits through grid‐electricity displacement. In an IDB system, biogas from the wastewater treatment facility is also upgraded to biomethane and used as a transportation biofuel. The GHG savings per unit of cropland in the IDB systems (2.7–2.9 MgCO₂/ha) are 1.5–1.6 fold greater than those in a conventional centralized system (1.7–1.8 MgCO₂/ha). Importantly, the biofuel selling price in the IDBs is lower by 28–30 cents per gasoline‐equivalent liter than in the conventional centralized system. Furthermore, the total capital investment per annual biofuel volume in the IDB is much lower (by ~80%) than that in the conventional centralized system. Therefore, utilization of biomethane and residual solids in the IDB systems leads to much lower biofuel selling prices and significantly greater GHG savings per unit of cropland participating in the biorefinery system compared to the conventional centralized biorefineries.     

High‐resolution photo‐mosaic time‐series imagery for monitoring human use of an artificial reef

Successful marine management relies on understanding patterns of human use. However, obtaining data can be difficult and expensive given the widespread and variable nature of activities conducted. Remote camera systems are increasingly used to overcome cost limitations of conventional labour‐intensive methods. Still, most systems face trade‐offs between the spatial extent and resolution over which data are obtained, limiting their application. We trialed a novel methodology, CSIRO Ruggedized Autonomous Gigapixel System (CRAGS), for time series of high‐resolution photo‐mosaic (HRPM) imagery to estimate fine‐scale metrics of human activity at an artificial reef located 1.3 km from shore. We compared estimates obtained using the novel system to those produced with a web camera that concurrently monitored the site. We evaluated the effect of day type (weekday/weekend) and time of day on each of the systems and compared to estimates obtained from binocular observations. In general, both systems delivered similar estimates for the number of boats observed and to those obtained by binocular counts; these results were also unaffected by the type of day (weekend vs. weekday). CRAGS was able to determine additional information about the user type and party size that was not possible with the lower resolution webcam system. However, there was an effect of time of day as CRAGS suffered from poor image quality in early morning conditions as a result of fixed camera settings. Our field study provides proof of concept of use of this new cost‐effective monitoring tool for the remote collection of high‐resolution large‐extent data on patterns of human use at high temporal frequency.     

Model-based control for a demand-driven biogas production to cover residual load rises

The development of systems for energy storage and demand-driven energy production will be essential to enable the switch from fossil to renewable energy sources in future. To cover the residual load rises, a rigorous dynamic process model based on the Anaerobic Digestion Model No. 1 (ADM1) was applied to analyse the flexible operation of biogas plants. For this, the model was optimised and an operational concept for a demand-driven energy production was worked out. Different substrates were analysed, both by batch fermentation and Weende analysis with van Soest method, to determine the input data of the model. The lab results show that the substrates have got different degradation kinetics and biogas potentials. Finally, the ADM1 was extended with a feeding algorithm which is based on a PI controller. Essential feeding times and quantities of available substrates were calculated so that a biogas plant can cover a defined energy demand. The results prove that a flexible operation of biogas plants with a feeding strategy is possible.

     

The potential of methane‐oxidizing bacteria for applications in environmental biotechnology

Methanotrophic bacteria possess a unique set of enzymes enabling them to oxidize, degrade and transform organic molecules and synthesize new compounds. Therefore, they have great potential in environmental biotechnology. The application of these unique properties was demonstrated in three case studies: (i) Methane escaping from leaky gas pipes may lead to massive mortality of trees in urban areas. Lack of oxygen within the soil surrounding tree roots caused by methanotrophic activity was identified as one of the reasons for this phenomenon. The similarity between metabolic reactions performed by the key enzymes of methanotrophs (methane monooxygenase) and ammonium oxidizers (ammonium monooxygenase) might offer a solution to this problem by applying commercially available nitrification and urease inhibitors. (ii) Methanotrophs are able to co‐metabolically degrade contaminants such as low‐molecular‐weight‐chlorinated hydrocarbons in soil and water in the presence of methane. Batch and continuous trichloroethylene degradation experiments in laboratory‐scale reactors using Methylocystis sp. GB 14 were performed, partly with cells entrapped in a polymer matrix. (iii) Using a short, two‐stage pilot‐scale process, the intracellular polymer accumulation of poly‐β‐hydroxybutyrate (PHB) in methanotrophs reached a maximum of 52%. Interestingly, an ultra‐high‐molecular‐weight PHB of 3.1 MDa was accumulated under potassium deficiency. Under strictly controlled conditions (temperature, pH and methane supply) this process can be nonsterile because of the establishment of a stable microbial community (dominant species Methylocystis sp. GB 25 ≥86% by biomass). The possibility to substitute methane with biogas from renewable sources facilitates the development of a methane‐based PHB production process that yields a high‐quality biopolymer at competitive costs.     

A predictive high‐throughput scale‐down model of monoclonal antibody production in CHO cells

Multi‐factorial experimentation is essential in understanding the link between mammalian cell culture conditions and the glycoprotein product of any biomanufacturing process. This understanding is increasingly demanded as bioprocess development is influenced by the Quality by Design paradigm. We have developed a system that allows hundreds of micro‐bioreactors to be run in parallel under controlled conditions, enabling factorial experiments of much larger scope than is possible with traditional systems. A high‐throughput analytics workflow was also developed using commercially available instruments to obtain product quality information for each cell culture condition. The micro‐bioreactor system was tested by executing a factorial experiment varying four process parameters: pH, dissolved oxygen, feed supplement rate, and reduced glutathione level. A total of 180 micro‐bioreactors were run for 2 weeks during this DOE experiment to assess this scaled down micro‐bioreactor system as a high‐throughput tool for process development. Online measurements of pH, dissolved oxygen, and optical density were complemented by offline measurements of glucose, viability, titer, and product quality. Model accuracy was assessed by regressing the micro‐bioreactor results with those obtained in conventional 3 L bioreactors. Excellent agreement was observed between the micro‐bioreactor and the bench‐top bioreactor. The micro‐bioreactor results were further analyzed to link parameter manipulations to process outcomes via leverage plots, and to examine the interactions between process parameters. The results show that feed supplement rate has a significant effect (P < 0.05) on all performance metrics with higher feed rates resulting in greater cell mass and product titer. Culture pH impacted terminal integrated viable cell concentration, titer and intact immunoglobulin G titer, with better results obtained at the lower pH set point. The results demonstrate that a micro‐scale system can be an excellent model of larger scale systems, while providing data sets broader and deeper than are available by traditional methods. Biotechnol. Bioeng. 2009; 104: 1107–1120. © 2009 Wiley Periodicals, Inc.     

Graphene–Polymer Nanocomposite‐Based Redox‐Induced Electricity for Flexible Self‐Powered Strain Sensors

Graphene as a powerful inorganic material such as excellent conductivity and ideal mechanical strength has recently been extensively utilized to develop flexible strain sensors. However, graphene‐based strain sensors usually suffer from the deficiencies of stretchability, sensitivity, and sensing range, which can restrict their applications in wearable devices. Here, a novel strain sensor is designed by integrating graphene/ecoflex film and meandering zinc wire into the flexible base. The constructed strain sensor not only possesses high stretchability of up to 150% strain but can also self‐generates current signals from redox‐induced electricity, where the stable current and voltage signals of about 75 µA and 0.83 V can be obtained, respectively. Furthermore, the self‐powered sensor presents a broad and linear sensing range of 25% to 150% strains and a fast response time of less than 0.11 s. Attached on human body, the sensor has been utilized to realize the motion detection of knee joint.     

Blood‐Capillary‐Inspired,Free‐Standing,Flexible, and Low‐Cost Super‐Hydrophobic N‐CNTs@SS Cathodes for High‐Capacity,High‐Rate,and Stable Li‐Air Batteries

With the rising demand for flexible and wearable electronic devices, flexible power sources with high energy densities are required to provide a sustainable energy supply. Theoretically, rechargeable, flexible Li‐O₂/air batteries can provide extremely high specific energy densities; however, the high costs, complex synthetic methods, and inferior mechanical properties of the available flexible cathodes severely limit their practical applications. Herein, inspired by the structure of human blood capillary tissue, this study demonstrates for the first time the in situ growth of interpenetrative hierarchical N‐doped carbon nanotubes on the surface of stainless‐steel mesh (N‐CNTs@SS) for the fabrication of a self‐supporting, flexible electrode with excellent physicochemical properties via a facile and scalable one‐step strategy. Benefitting from the synergistic effects of the high electronic conductivity and stable 3D interconnected conductive network structure, the Li‐O₂ batteries obtained with the N‐CNTs@SS cathode exhibit superior electrochemical performance, including a high specific capacity (9299 mA h g^?1 at 500 mA g^?1), an excellent rate capability, and an exceptional cycle stability (up to 232 cycles). Furthermore, as‐fabricated flexible Li‐air batteries containing the as‐prepared flexible super‐hydrophobic cathode show excellent mechanical properties, stable electrochemical performance, and superior H₂O resistibility, which enhance their potential to power flexible and wearable electronic devices.     

3D Macroporous Nitrogen‐Enriched Graphitic Carbon Scaffold for Efficient Bioelectricity Generation in Microbial Fuel Cells

Microbial fuel cell (MFC) can generate electricity based on oxidation of organic compounds by exoelectogens, giving rise to a promising potential for recovering electrical energy from organic wastewater. The structure and property of anode materials have inherent impact to extracellular electron transfer (EET), an interfacial process that greatly limits bioelectricity production of MFC. Herein, a three dimensional (3D) macroporous nitrogen‐enriched graphitic carbon (NGC) scaffold is fabricated from commercially available melamine foam using facile pyrolysis method. The NGC electrode is demonstrated to promote EET ef?ciently, achieving a power density of 750 mW m^?2 based on pure cultured Shewanella oneidensis MR‐1 in acetate‐feeding MFC. The unique 3D open‐cell structure not only offers habitats for colonization of electroactive bio?lm up to a maximal density but also provides macroporous architecture for internal mass transfer without concern of bio‐blocking and bio‐fouling. Additionally, nitrogen incorporation also plays a signi?cant role in enhancing EET, where pyrrolic nitrogen is much more active than graphitic and pyridinic nitrogen as indicated by density functional theory calculation. This work provides a proof‐of‐concept demonstration of a high‐ef?ciency, cost‐effective, easily scaling‐up, and environmentally friendly anode material of bioelectrochemical systems for electricity generation, hydrogen production, and pollutant degradation.     

Adapting Stand‐Alone Renewable Energy Technologies for the Circular Economy through Eco‐Design and Recycling

Renewable energy (RE) technologies are looked upon favorably to provide for future energy demands and reduce greenhouse gas (GHG) emissions. However, the installation of these technologies requires large quantities of finite material resources. We apply life cycle assessment to 100 years of electricity generation from three stand‐alone RE technologies—solar photovoltaics, run‐of‐river hydro, and wind—to evaluate environmental burden profiles against baseline electricity generation from fossil fuels. We then devised scenarios to incorporate circular economy (CE) improvements targeting hotspots in systems’ life cycle, specifically (1) improved recycling rates for raw materials and (ii) the application of eco‐design. Hydro presented the lowest environmental burdens per kilowatt‐hour of electricity generation compared with other RE technologies, owing to its higher efficiency and longer life spans for main components. Distinct results were observed in the environmental performance of each system based on the consideration of improved recycling rates and eco‐design. CE measures produced similar modest savings in already low GHG emissions burdens for each technology, while eco‐design specifically had the potential to provide significant savings in abiotic resource depletion. Further research to explore the full potential of CE measures for RE technologies will curtail the resource intensity of RE technologies required to mitigate climate change.     

Green electricity and biowastes via biogas to bulk‐chemicals and fuels: The next move toward a sustainable bioeconomy

To deal with the global challenges of limited fossil resources, climate change, and environmental pollution bioeconomy has been identified globally as a strategic development goal. In this regard, many industrial countries and regions have set very ambiguous targets: e.g. within the EU 25–30% of all chemicals and other industrial products as well as 5–10% of transportation fuels should be bio‐based by 2030. These targets are hardly achievable and not sustainable with presently known bio‐production systems, mainly due to constrains in substrate availability, limited product yield, and high processing costs. Thus, new concepts are desperately needed. Against this background, an innovative and sustainable concept is presented and discussed here. The central idea of the concept is the conversion of organic wastes into a widely usable product—biogas (CO₂ +CH₄)—which is then used as a clean and uniform substrate for the synthesis of bulk‐chemicals and/or fuels, especially by using green electricity from wind and solar. Such a concept (shortened as E&G²C) has the potential to overcome major limitations of known bioproduction systems. Biogas as a substrate of biosynthesis has many unique advantages, including sustainability, efficiency, and flexibility. The use of electricity for biosynthesis with biogas represents an ideal system for efficient bioelectrochemical conversion. Here, the rationale behind the concept is illustrated, its sustainability is underpinned with concrete data, and the realization of the concept is discussed by looking at the possible conversion routes and key issues to be solved. The markets and perspectives provided by the concept E&G²C are also briefly addressed. In conclusion, the concept E&G²C provides a unique and innovative path for the next move toward a real sustainable bioeconomy.     

Enhanced contrast acoustic‐resolution photoacoustic microscopy using double‐stage delay‐multiply‐and‐sum beamformer for vasculature imaging

In acoustic‐resolution photoacoustic microscopy (AR‐PAM) systems, the lateral resolution in the focal zone of the ultrasound (US) transducer is determined by the numerical aperture (NA) of the transducer. To have a high lateral resolution, a large NA is used. However, the larger the NA, the smaller the depth of focus [DOF]. As a result, the lateral resolution is deteriorated at depths out of the focal region. The synthetic aperture focusing technique (SAFT) along with a beamformer can be used to improve the resolution outside the focal region. In this work, for image formation in AR‐PAM, we propose the double‐stage delay‐multiply‐and‐sum (DS_DMAS) algorithm to be combined with SAFT. The proposed method is evaluated experimentally using hair targets and in vivo vasculature imaging. It is shown that DS_DMAS provides a higher resolution and contrast compared to other methods. For the B‐mode images obtained using the hair phantom, the proposed method reduces the average noise level for all the depths by about 134%, 57% and 23%, compared to the original low‐ resolution, SAFT+DAS and SAFT+DMAS methods, respectively. All the results indicate that the proposed method can be an appropriate algorithm for image formation in AR‐PAM systems.      

All‐Inkjet‐Printed,All‐Air‐Processed Solar Cells

The prospective of using direct‐write printing techniques for the manufacture of organic photovoltaics (OPVs) has made these techniques highly attractive. OPVs have the potential to revolutionize small‐scale portable electronic applications by directly providing electric power to the systems. However, no route is available for monolithically integrating the energy‐harvesting units into a system in which other components, such as transistors, sensors, or displays, are already fabricated. Here, the fabrication and the measurement of inkjet‐printed, air‐processed organic solar cells is reported for the first time. Highly controlled conducting and semiconducting films using engineered inks for inkjet printing enable good efficiencies for printed OPVs between ≈2 and 5% power conversion efficiency. The results show that inkjet printing is an attractive digital printing technology for cost‐effective, environmentally friendly integration of photovoltaic cells onto plastic substrates.     

Homology‐based hydrogen bond information improves crystallographic structures in the PDB

The Protein Data Bank (PDB) is the global archive for structural information on macromolecules, and a popular resource for researchers, teachers, and students, amassing more than one million unique users each year. Crystallographic structure models in the PDB (more than 100,000 entries) are optimized against the crystal diffraction data and geometrical restraints. This process of crystallographic refinement typically ignored hydrogen bond (H‐bond) distances as a source of information. However, H‐bond restraints can improve structures at low resolution where diffraction data are limited. To improve low‐resolution structure refinement, we present methods for deriving H‐bond information either globally from well‐refined high‐resolution structures from the PDB‐REDO databank, or specifically from on‐the‐fly constructed sets of homologous high‐resolution structures. Refinement incorporating HOmology DErived Restraints (HODER), improves geometrical quality and the fit to the diffraction data for many low‐resolution structures. To make these improvements readily available to the general public, we applied our new algorithms to all crystallographic structures in the PDB: using massively parallel computing, we constructed a new instance of the PDB‐REDO databank ( https://pdb-redo.eu ). This resource is useful for researchers to gain insight on individual structures, on specific protein families (as we demonstrate with examples), and on general features of protein structure using data mining approaches on a uniformly treated dataset.     

Revival of the biological sunlight‐to‐biogas energy conversion system

In the quest for renewable resources, algae are increasingly receiving attention. Their high growth rate, high CO₂ fixation and their lack of requirement for fertile soil surface represent several advantages as compared to conventional (energy) crops. Through their ability to store large amounts of oils, they qualify as a source for biodiesel. Algal biomass, however, can also be used as such, namely as a substrate for anaerobic digestion. In the present research, we investigated the use of algae for energy generation in a stand‐alone, closed‐loop system. The system encompasses an algal growth unit for biomass production, an anaerobic digestion unit to convert the biomass to biogas and a microbial fuel cell to polish the effluent of the digester. Nutrients set free during digestion can accordingly be returned to the algal growth unit for a sustained algal growth. Hence, a system is presented that continuously transforms solar energy into energy‐rich biogas and electricity. Algal productivities of 24–30 ton VS ha^?1 year^?1 were reached, while 0.5 N m³ biogas could be produced kg^?1 algal VS. The system described resulted in a power plant with a potential capacity of about 9 kW ha^?1 of solar algal panel, with prospects of 23 kW ha^?1. Biotechnol. Bioeng. 2009;103: 296–304. © 2009 Wiley Periodicals, Inc.     

Integrated biogas upgrading and hydrogen utilization in an anaerobic reactor containing enriched hydrogenotrophic methanogenic culture

Biogas produced by anaerobic digestion, is mainly used in a gas motor for heat and electricity production. However, after removal of CO₂, biogas can be upgraded to natural gas quality, giving more utilization possibilities, such as utilization as autogas, or distant utilization by using the existing natural gas grid. The current study presents a new biological method for biogas upgrading in a separate biogas reactor, containing enriched hydrogenotrophic methanogens and fed with biogas and hydrogen. Both mesophilic‐ and thermophilic anaerobic cultures were enriched to convert CO₂ to CH₄ by addition of H₂. Enrichment at thermophilic temperature (55°C) resulted in CO₂ and H₂ bioconversion rate of 320 mL CH₄/(gVSS h), which was more than 60% higher than that under mesophilic temperature (37°C). Different dominant species were found at mesophilic‐ and thermophilic‐enriched cultures, as revealed by PCR–DGGE. Nonetheless, they all belonged to the order Methanobacteriales, which can mediate hydrogenotrophic methanogenesis. Biogas upgrading was then tested in a thermophilic anaerobic reactor under various operation conditions. By continuous addition of hydrogen in the biogas reactor, high degree of biogas upgrading was achieved. The produced biogas had a CH₄ content, around 95% at steady‐state, at gas (mixture of biogas and hydrogen) injection rate of 6 L/(L day). The increase of gas injection rate to 12 L/(L day) resulted in the decrease of CH₄ content to around 90%. Further study showed that by decreasing the gas–liquid mass transfer by increasing the stirring speed of the mixture the CH₄ content was increased to around 95%. Finally, the CH₄ content around 90% was achieved in this study with the gas injection rate as high as 24 L/(L day). Biotechnol. Bioeng. 2012; 109: 2729–2736. © 2012 Wiley Periodicals, Inc.     

QCMAP: An Interactive Web‐Tool for Performance Diagnosis and Prediction of LC‐MS Systems

The increasing role played by liquid chromatography‐mass spectrometry (LC‐MS)‐based proteomics in biological discovery has led to a growing need for quality control (QC) on the LC‐MS systems. While numerous quality control tools have been developed to track the performance of LC‐MS systems based on a pre‐defined set of performance factors (e.g., mass error, retention time), the precise influence and contribution of the performance factors and their generalization property to different biological samples are not as well characterized. Here, a web‐based application (QCMAP) is developed for interactive diagnosis and prediction of the performance of LC‐MS systems across different biological sample types. Leveraging on a standardized HeLa cell sample run as QC within a multi‐user facility, predictive models are trained on a panel of commonly used performance factors to pinpoint the precise conditions to a (un)satisfactory performance in three LC‐MS systems. It is demonstrated that the learned model can be applied to predict LC‐MS system performance for brain samples generated from an independent study. By compiling these predictive models into our web‐application, QCMAP allows users to benchmark the performance of their LC‐MS systems using their own samples and identify key factors for instrument optimization. QCMAP is freely available from: http://shiny.maths.usyd.edu.au/QCMAP/ .     

Plasmid‐free T7‐based Escherichia coli expression systems

In order to release host cells from plasmid‐mediated increases in metabolic load and high gene dosages, we developed a plasmid‐free, T7‐based E. coli expression system in which the target gene is site‐specifically integrated into the genome of the host. With this system, plasmid‐loss, a source of instability for conventional expression systems, was eliminated. At the same time, system leakiness, a challenging problem with recombinant systems, was minimized. The efficiency of the T7 RNA polymerase compensates for low gene dosage and provides high rates of recombinant gene expression without fatal consequences to host metabolism. Relative to conventional pET systems, this system permits improved process stability and increases the host cell's capacity for recombinant gene expression, resulting in higher product yields. The stability of the plasmid‐free system was proven in chemostat cultivation for 40 generations in a non‐induced and for 10 generations in a fully induced state. For this reason plasmid‐free systems benefit the development of continuous production processes with E. coli. However, time and effort of the more complex cloning procedure have to be considered in relation to the advantages of plasmid‐free systems in upstream‐processing. Biotechnol. Bioeng. 2010. 105: 786–794. © 2009 Wiley Periodicals, Inc.     

Solvated protein–protein docking using Kyte‐Doolittle‐based water preferences

HADDOCK is one of the few docking programs that can explicitly account for water molecules in the docking process. Its solvated docking protocol starts from hydrated molecules and a fraction of the resulting interfacial waters is subsequently removed in a biased Monte Carlo procedure based on water‐mediated contact probabilities. The latter were derived from an analysis of water contact frequencies from high‐resolution crystal structures. Here, we introduce a simple water‐mediated amino acid–amino acid contact probability scale derived from the Kyte‐Doolittle hydrophobicity scale and assess its performance on the largest high‐resolution dataset developed to date for solvated docking. Both scales yield high‐quality docking results. The novel and simple hydrophobicity scale, which should reflect better the physicochemical principles underlying contact propensities, leads to a performance improvement of around 10% in ranking, cluster quality and water recovery at the interface compared with the statistics‐based original solvated docking protocol. Proteins 2013. © 2012 Wiley Periodicals, Inc.     

Self‐Contained Monolithic Carbon Sponges for Solar‐Driven Interfacial Water Evaporation Distillation and Electricity Generation

Solar vaporization has received tremendous attention for its potential in desalination, sterilization, distillation, etc. However, a few major roadblocks toward practical application are the high cost, process intensive, fragility of solar absorber materials, and low efficiency. Herein an inexpensive cellular carbon sponge that has a broadband light absorption and inbuilt structural features to perform solitary heat localization for in situ photothermic vaporization is reported. The defining advantages of elastic cellular porous sponge are that it self‐confines water to the perpetually hot spots and accommodates cyclical dynamic fluid flow‐volume variable stress for practical usage. By isolating from bulk water, the solar‐to‐vapor conversion efficiency is increased by 2.5‐fold, surpassing that of conventional bulk heating. Notably, complementary solar steam generation‐induced electricity can be harvested during the solar vaporization so as to capitalize on waste heat. Such solar distillation and waste heat‐to‐electricity generation functions may provide potential opportunities for on‐site electricity and fresh water production for remote areas/emergency needs.     

Sub‐angstrom modeling of complexes between flexible peptides and globular proteins

A wide range of regulatory processes in the cell are mediated by flexible peptides that fold upon binding to globular proteins. Computational efforts to model these interactions are hindered by the large number of rotatable bonds in flexible peptides relative to typical ligand molecules, and the fact that different peptides assume different backbone conformations within the same binding site. In this study, we present Rosetta FlexPepDock, a novel tool for refining coarse peptide–protein models that allows significant changes in both peptide backbone and side chains. We obtain high resolution models, often of sub‐angstrom backbone quality, over an extensive and general benchmark that is based on a large nonredundant dataset of 89 peptide–protein interactions. Importantly, side chains of known binding motifs are modeled particularly well, typically with atomic accuracy. In addition, our protocol has improved modeling quality for the important application of cross docking to PDZ domains. We anticipate that the ability to create high resolution models for a wide range of peptide–protein complexes will have significant impact on structure‐based functional characterization, controlled manipulation of peptide interactions, and on peptide‐based drug design. Proteins 2010. © 2010 Wiley‐Liss, Inc.