標(biāo)題: Titlebook: Computational Peptide Science; Methods and Protocol Thomas Simonson Book 2022 The Editor(s) (if applicable) and The Author(s), under exclus [打印本頁] 作者: Cession 時(shí)間: 2025-3-21 18:12
書目名稱Computational Peptide Science影響因子(影響力)
作者: 改革運(yùn)動(dòng) 時(shí)間: 2025-3-21 20:45 作者: V切開 時(shí)間: 2025-3-22 03:20 作者: Synchronism 時(shí)間: 2025-3-22 04:37
Excited Nuclear States for He-10 (Helium),d at understanding the early aggregation steps of short linear amyloid peptides, the conformational ensemble of the Aβ40/42 dimers in bulk solution, and the stability of Aβ aggregates in lipid membrane models. Then we focus on our studies on the interactions of amyloid peptides/inhibitors to prevent作者: 詼諧 時(shí)間: 2025-3-22 10:41
Excited Nuclear States for Li-8 (Lithium),er, we describe how to utilize MD simulations to predict and study peptide dynamics and how to validate the simulations by circular dichroism, intrinsic fluorescent probe, membrane leakage assay, electrical impedance, and isothermal titration calorimetry. Experimentally validated MD simulations open作者: exigent 時(shí)間: 2025-3-22 16:01
Excited Nuclear States for He-6 (Helium), prior to the matching. This extension allows one to reduce the amount of evaluated putative cyclic peptides and to specifically design only those that compete with the strongest protein–protein binding regions. It is illustrated by an application to an MHC class I protein complex.作者: exigent 時(shí)間: 2025-3-22 21:02 作者: Outshine 時(shí)間: 2025-3-22 21:16 作者: 花費(fèi) 時(shí)間: 2025-3-23 02:18
Excited Nuclear States for He-3 (Helium),r Proteus software, as a detailed downloadable tutorial. The unfolded model is combined with a folded model that uses molecular mechanics and a Generalized Born solvent. It was optimized for three PDZ domains and then used to redesign them. The sequences sampled are native-like and similar to a rece作者: Mri485 時(shí)間: 2025-3-23 07:17
Machine Learning Prediction of Antimicrobial Peptides,multiple functional roles of AMPs annotated in the APD also enabled multi-label predictions (iAMP-2L, MLAMP, and AMAP), which include antibacterial, antiviral, antifungal, antiparasitic, antibiofilm, anticancer, anti-HIV, antimalarial, insecticidal, antioxidant, chemotactic, spermicidal activities, 作者: Astigmatism 時(shí)間: 2025-3-23 10:13
Exploring the Peptide Potential of Genomes,ims to explore the potential of a genome to produce novel peptides. It consists in annotating all the open reading frames (ORFs) of a genome (i.e., coding and noncoding ones) and characterizing the fold potential and other structural properties of their corresponding potential peptides. Here, we app作者: delusion 時(shí)間: 2025-3-23 15:44 作者: OMIT 時(shí)間: 2025-3-23 20:29 作者: facetious 時(shí)間: 2025-3-23 23:39
Predicting Membrane-Active Peptide Dynamics in Fluidic Lipid Membranes,er, we describe how to utilize MD simulations to predict and study peptide dynamics and how to validate the simulations by circular dichroism, intrinsic fluorescent probe, membrane leakage assay, electrical impedance, and isothermal titration calorimetry. Experimentally validated MD simulations open作者: Amorous 時(shí)間: 2025-3-24 02:32
,Rapid Rational Design of Cyclic Peptides Mimicking Protein–Protein Interfaces, prior to the matching. This extension allows one to reduce the amount of evaluated putative cyclic peptides and to specifically design only those that compete with the strongest protein–protein binding regions. It is illustrated by an application to an MHC class I protein complex.作者: Synchronism 時(shí)間: 2025-3-24 07:17
,Structural Prediction of Peptide–MHC Binding Modes,g of the molecular mechanisms triggering the immunological processes, estimating peptide/MHC affinity using universal physics-based approaches, and driving the design of novel peptide ligands. Unfortunately, due to the large diversity of MHC allotypes and possible peptides, the growing number of 3D 作者: 一個(gè)姐姐 時(shí)間: 2025-3-24 12:44
Computational Design of Miniprotein Binders,tic targets. The computational pipeline exploits provable and deterministic artificial intelligence-based protein design methods, with some recent additions in terms of binding energy estimation, multistate design and diverse library generation.作者: Gudgeon 時(shí)間: 2025-3-24 18:48
Knowledge-Based Unfolded State Model for Protein Design,r Proteus software, as a detailed downloadable tutorial. The unfolded model is combined with a folded model that uses molecular mechanics and a Generalized Born solvent. It was optimized for three PDZ domains and then used to redesign them. The sequences sampled are native-like and similar to a rece作者: 哀求 時(shí)間: 2025-3-24 19:57 作者: Certainty 時(shí)間: 2025-3-25 02:44
1064-3745 ation advice from the experts.This volume details current and new computational methodologies to study peptides.? Chapters guide readers through antimicrobial peptides, foldability, amyloid sheet formation, membrane-active peptides, organized peptide assemblies, protein-peptide interfaces, predictio作者: detach 時(shí)間: 2025-3-25 05:45
Excited Nuclear States for Li-8 (Lithium),d-switching proteins, properties of protein–protein interfaces, quantifying sphericity, helping to improve protein–protein docking scores, and estimating the effect of mutations on stability. A conjecture about the Achilles’ heel of proteins is presented as well.作者: 珠寶 時(shí)間: 2025-3-25 10:02 作者: 指耕作 時(shí)間: 2025-3-25 14:24
Tools for Characterizing Proteins: Circular Variance, Mutual Proximity, Chameleon Sequences, and Sud-switching proteins, properties of protein–protein interfaces, quantifying sphericity, helping to improve protein–protein docking scores, and estimating the effect of mutations on stability. A conjecture about the Achilles’ heel of proteins is presented as well.作者: 過渡時(shí)期 時(shí)間: 2025-3-25 19:08
Free Energy-Based Computational Methods for the Study of Protein-Peptide Binding Equilibria,y estimation with implicit solvation, (2) alchemical relative binding free energy estimation with explicit solvation, and (3) potential of mean force binding free energy estimation. Case studies of protein-peptide binding application taken from the recent literature are discussed for each method.作者: 突襲 時(shí)間: 2025-3-25 23:50 作者: irreducible 時(shí)間: 2025-3-26 01:54 作者: 出生 時(shí)間: 2025-3-26 04:37
Book 2022tational Peptides Science: Methods and Protocols .aims to provide concepts, methods, and guidelines to help both novices and experienced workers benefit from today‘s new opportunities and challenges..作者: 圓柱 時(shí)間: 2025-3-26 08:58
Excited Nuclear States for He-7 (Helium),ethods to two peptides that have an intrinsically disordered nature, the histone H3 and H4 N-terminal tails, and use metadynamics to compute the free energy landscape along collective variables discerned from aMD simulations. Results show that these peptides are largely disordered, with a slight preference for α-helical structures.作者: landfill 時(shí)間: 2025-3-26 15:10
https://doi.org/10.1007/978-3-662-48875-1nd approaches used for identifying and optimizing peptides that target protein-protein interfaces with high affinity and specificity. We hope that this review will help to implement appropriate in silico strategies for peptide-based drug design that builds on available information for the systems of interest.作者: condone 時(shí)間: 2025-3-26 17:04
Excited Nuclear States for H-2 (Hydrogen),c tutorial to run the code for an antibody fragment design example. Finally, we describe three additional applications of the method to design peptides for different targets, illustrating the broad scope of the proposed approach.作者: 松雞 時(shí)間: 2025-3-26 21:27
Peptide Dynamics and Metadynamics: Leveraging Enhanced Sampling Molecular Dynamics to Robustly Modeethods to two peptides that have an intrinsically disordered nature, the histone H3 and H4 N-terminal tails, and use metadynamics to compute the free energy landscape along collective variables discerned from aMD simulations. Results show that these peptides are largely disordered, with a slight preference for α-helical structures.作者: Inculcate 時(shí)間: 2025-3-27 01:19
Computational Tools and Strategies to Develop Peptide-Based Inhibitors of Protein-Protein Interactind approaches used for identifying and optimizing peptides that target protein-protein interfaces with high affinity and specificity. We hope that this review will help to implement appropriate in silico strategies for peptide-based drug design that builds on available information for the systems of interest.作者: Strength 時(shí)間: 2025-3-27 06:14
Computational Evolution Protocol for Peptide Design,c tutorial to run the code for an antibody fragment design example. Finally, we describe three additional applications of the method to design peptides for different targets, illustrating the broad scope of the proposed approach.作者: 未成熟 時(shí)間: 2025-3-27 11:40
Excited Nuclear States for Li-7 (Lithium),ful control of peptide freedom to promote optimal membrane adsorption before other interactions are allowed. This shortens preparation times prior to production simulations while avoiding divergence into unrealistic or artifactual configurations.作者: 舉止粗野的人 時(shí)間: 2025-3-27 14:31
Excited Nuclear States for He-7 (Helium),KID). The structural properties of free pKID and KID were obtained by parallel tempering metadynamics combined with well-tempered ensemble (PTMetaD WTE) method, and the binding free energy surfaces of pKID/KID and KIX were characterized by bias-exchanged metadynamics (BE-MetaD) simulations.作者: Decrepit 時(shí)間: 2025-3-27 19:12 作者: ELUC 時(shí)間: 2025-3-28 01:51
Excited Nuclear States for H-2 (Hydrogen), scale. The obtained sequences are filtered in terms of the affinity and the stability of the complex. In the second stage, design sequences are further evaluated by all-atom molecular dynamics simulations and binding free energy calculations with a molecular mechanics/implicit solvent free energy function.作者: mechanical 時(shí)間: 2025-3-28 02:17
Coarse-Grain Simulations of Membrane-Adsorbed Helical Peptides,ful control of peptide freedom to promote optimal membrane adsorption before other interactions are allowed. This shortens preparation times prior to production simulations while avoiding divergence into unrealistic or artifactual configurations.作者: 聯(lián)想 時(shí)間: 2025-3-28 06:21 作者: Melatonin 時(shí)間: 2025-3-28 12:19
Molecular Simulation of Stapled Peptides, describe the procedures for performing and analyzing MD simulations of hydrocarbon-stapled peptides using the CHARMM energy function, in isolation and in complex with a binding partner, to investigate their conformational properties and to compute changes in their binding affinity upon mutation.作者: 巨碩 時(shí)間: 2025-3-28 16:44 作者: 貪婪的人 時(shí)間: 2025-3-28 21:39 作者: exigent 時(shí)間: 2025-3-29 02:34 作者: BRAND 時(shí)間: 2025-3-29 04:56
Tools for Characterizing Proteins: Circular Variance, Mutual Proximity, Chameleon Sequences, and Suproximity, and a subsequence-based foldability score. These concepts were used in estimating foldability of globular, intrinsically disordered and fold-switching proteins, properties of protein–protein interfaces, quantifying sphericity, helping to improve protein–protein docking scores, and estimat作者: SEVER 時(shí)間: 2025-3-29 10:04
Exploring the Peptide Potential of Genomes, the pervasive translation of the resulting RNAs offer to the organisms a vast reservoir of novel peptides. Although the majority of these peptides are anticipated as deleterious or neutral, and thereby expected to be degraded right away or short-lived in evolutionary history, some of them can confe作者: 鳴叫 時(shí)間: 2025-3-29 13:21
,Computational Identification and Design of Complementary β-Strand Sequences,l processes, and some are known to be related to serious diseases such as neurologic disorders and amyloidosis. The self-assembly of ?-sheet peptides also has practical applications in material sciences since they can be building blocks of repeated nanostructures. Therefore, computational algorithms作者: BOOR 時(shí)間: 2025-3-29 18:34 作者: STYX 時(shí)間: 2025-3-29 20:45
Predicting Membrane-Active Peptide Dynamics in Fluidic Lipid Membranes,for infections but also be applied to finding targeted therapies for cancer and other diseases. However, designing biophysical experiments to study molecular interactions between flexible peptides and fluidic lipid membranes has been an ongoing challenge. Recently, with hardware advances, algorithm 作者: Pandemic 時(shí)間: 2025-3-30 01:47 作者: 蔓藤圖飾 時(shí)間: 2025-3-30 06:31
Peptide Dynamics and Metadynamics: Leveraging Enhanced Sampling Molecular Dynamics to Robustly ModeHowever, even with modern computing power, they are limited in the timescales they can sample, which is especially problematic for peptides that are fully or partially disordered. Here, we discuss how the enhanced sampling methods accelerated molecular dynamics (aMD) and metadynamics can be leverage作者: defray 時(shí)間: 2025-3-30 11:06 作者: Defraud 時(shí)間: 2025-3-30 15:40
Computational and Experimental Protocols to Study Cyclo-dihistidine Self- and Co-assembly: Minimaliinescence and their ability to self-encapsulate epirubicin, a chemotherapy drug. Here, we provide a detailed description of computational and experimental methodology for the study of cyclo-HH self- and co-assembling mechanisms, photoluminescence, and drug encapsulation properties. We outline the ex作者: Acquired 時(shí)間: 2025-3-30 17:53
Computational Tools and Strategies to Develop Peptide-Based Inhibitors of Protein-Protein Interacti severe diseases. Peptide derivatives are very promising therapeutic agents for modulating protein-protein associations with sizes and specificities between those of small compounds and antibodies. For the same reasons, rational design of peptide-based inhibitors naturally borrows and combines compu作者: 放棄 時(shí)間: 2025-3-30 22:55
,Rapid Rational Design of Cyclic Peptides Mimicking Protein–Protein Interfaces,terfaces. The method selects cyclic peptides that structurally match backbone structures of short segments at a protein–protein interface. In a second step, the cyclic peptides act as templates for designed binders by adapting the amino acid side chains to the side chains found in the target complex作者: 泄露 時(shí)間: 2025-3-31 01:16 作者: jet-lag 時(shí)間: 2025-3-31 06:05
Molecular Simulation of Stapled Peptides,cule drugs, and of designed antibodies. Because of their modest size, the rational design of such peptides is becoming increasingly amenable to computer simulation; multi-microsecond molecular dynamic (MD) simulations are now routinely possible on consumer-grade graphical processors (GPUs). Here, we作者: AUGUR 時(shí)間: 2025-3-31 11:35 作者: AVOID 時(shí)間: 2025-3-31 14:43
Computational Evolution Protocol for Peptide Design,y is describing accurately the peptide–target interactions at the molecular level. We here review a computational peptide design protocol whose key feature is the use of all-atom explicit solvent molecular dynamics for describing the different peptide–target complexes explored during the optimizatio作者: tangle 時(shí)間: 2025-3-31 21:07
Computational Design of Miniprotein Binders,onal antibodies, they can be designed to bind to therapeutic targets with high affinity, but they are more stable and easier to produce and to administer. In this chapter, we present a structure-based computational generic approach for miniprotein inhibitor design. Specifically, we describe step-by-作者: Ledger 時(shí)間: 2025-4-1 01:14 作者: 織布機(jī) 時(shí)間: 2025-4-1 03:57 作者: Eclampsia 時(shí)間: 2025-4-1 08:48
Thomas SimonsonIncludes cutting-edge methods and protocols.Provides step-by-step detail essential for reproducible results.Contains key notes and implementation advice from the experts作者: reflection 時(shí)間: 2025-4-1 13:44
Methods in Molecular Biologyhttp://image.papertrans.cn/c/image/232888.jpg作者: BLANC 時(shí)間: 2025-4-1 17:10
