Journal of Computational Chemistry最新文献_第3页

Elongation Method-Based Alternating Multi-Directional Automated Property Optimization Process and Its Application

IF 3.4 3区化学

Journal of Computational Chemistry Pub Date : 2025-02-08 DOI: 10.1002/jcc.70058

Shichen Lin, Yuuichi Orimoto, Yuriko Aoki

{"title":"Elongation Method-Based Alternating Multi-Directional Automated Property Optimization Process and Its Application","authors":"Shichen Lin, Yuuichi Orimoto, Yuriko Aoki","doi":"10.1002/jcc.70058","DOIUrl":"https://doi.org/10.1002/jcc.70058","url":null,"abstract":"<div>\u0000 \u0000 Elongation (ELG) method-based property optimization (POPT) is an effective approach for designing large systems from one terminal to the other. An alternating multi-directional ELG method is introduced to enable alternating POPT for complex systems with multiple growth directions, improving efficiency. (Hyper)polarizabilities of donor-acceptor-substituted polydiacetylenes (PDAs) aligned along the <math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>z</mi>\u0000 </mrow>\u0000 <annotation>$$ z $$</annotation>\u0000 </semantics></math>-axis are optimized by alternating POPT, where donor- and acceptor-substituted diacetylene monomers are alternately selected and attached to two PDA terminals. Alternating POPT's capability in designing systems with expected properties, efficiency, and accuracy has been validated. For <math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>n</mi>\u0000 </mrow>\u0000 <annotation>$$ n $$</annotation>\u0000 </semantics></math> types of donor and acceptor groups, the existing simultaneous ELG-based POPT requires calculating <math>\u0000 <semantics>\u0000 <mrow>\u0000 <msup>\u0000 <mrow>\u0000 <mi>n</mi>\u0000 </mrow>\u0000 <mrow>\u0000 <mn>2</mn>\u0000 </mrow>\u0000 </msup>\u0000 </mrow>\u0000 <annotation>$$ {n}^2 $$</annotation>\u0000 </semantics></math> combinations, as monomers are simultaneously attached in both elongation directions. In contrast, the alternating ELG-based POPT only requires <math>\u0000 <semantics>\u0000 <mrow>\u0000 <mn>2</mn>\u0000 <mi>n</mi>\u0000 </mrow>\u0000 <annotation>$$ 2n $$</annotation>\u0000 </semantics></math> combinations, halving the number of basis functions involved in calculations and significantly enhancing efficiency.\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 5","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143370083","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A Robust and Versatile QM/MM Interface for Molecular Dynamics in GROMOS

IF 3.4 3区化学

Journal of Computational Chemistry Pub Date : 2025-02-07 DOI: 10.1002/jcc.70053

Peter Poliak, Patrick Bleiziffer, Felix Pultar, Sereina Riniker, Chris Oostenbrink

{"title":"A Robust and Versatile QM/MM Interface for Molecular Dynamics in GROMOS","authors":"Peter Poliak, Patrick Bleiziffer, Felix Pultar, Sereina Riniker, Chris Oostenbrink","doi":"10.1002/jcc.70053","DOIUrl":"10.1002/jcc.70053","url":null,"abstract":"The integration of quantum mechanics and molecular mechanics (QM/MM) within molecular dynamics simulations is crucial to accurately model complex biochemical systems. Here, we present an enhanced implementation of the QM/MM interface in the GROMOS simulation package, introducing significant improvements in functionality and user control. We present new features, including the link atom scheme, which allows the modeling of QM regions as a part of bigger molecules. Benchmark tests on various systems, including QM water in water, amino acids in water, and tripeptides validate the reliability of the new functionalities. Performance evaluations demonstrate that the updated implementation is efficient, with the primary computational burden attributed to the QM program rather than the QM/MM interface or the MD program itself. The improved QM/MM interface enables more advanced investigations into biomolecular reactivity, enzyme catalysis, and other phenomena requiring detailed quantum mechanical treatment within classical simulations. This work represents a significant advancement in the capabilities of GROMOS, providing enhanced tools to explore complex molecular systems.","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 5","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70053","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143258578","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

AIMD-Based Protocols for Modeling Exciplex Fluorescence Spectra and Inter-System Crossing in Photocatalytic Chromophores

IF 3.4 3区化学

Journal of Computational Chemistry Pub Date : 2025-02-04 DOI: 10.1002/jcc.70049

Goran Giudetti, Shaama Mallikarjun Sharada, Anna I. Krylov

{"title":"AIMD-Based Protocols for Modeling Exciplex Fluorescence Spectra and Inter-System Crossing in Photocatalytic Chromophores","authors":"Goran Giudetti, Shaama Mallikarjun Sharada, Anna I. Krylov","doi":"10.1002/jcc.70049","DOIUrl":"10.1002/jcc.70049","url":null,"abstract":"<div>\u0000 \u0000 This study introduces a computational protocol for modeling the emission spectra of exciplexes using excited-state ab initio molecular dynamics (AIMD) simulations. The protocol is applied to a model exciplex formed by oligo-p-phenylenes (OPPs) and triethylamine (TEA), which is of interest in the context of photocatalytic reduction of <math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mrow>\u0000 <mtext>CO</mtext>\u0000 </mrow>\u0000 <mrow>\u0000 <mn>2</mn>\u0000 </mrow>\u0000 </msub>\u0000 </mrow>\u0000 <annotation>$$ {mathrm{CO}}_2 $$</annotation>\u0000 </semantics></math>. AIMD facilitates efficient sampling of the conformational space of OPP3 and OPP4 exciplexes with TEA, offering a dynamic alternative to previously employed static methods. The AIMD-based protocol successfully reproduces experimental emission spectra for OPP-TEA exciplexes, agreeing with previous computational and experimental findings. The results show that AIMD simulations provide an efficient means of sampling the conformational space of these exciplexes, requiring less user input and, in some instances, fewer computational resources than multiple excited-state optimizations initiated from user-specified initial structures. The study also evaluates the yield of intersystem crossing (ISC) using AIMD and Landau-Zener probability. The results suggest that ISC is a minor decay channel for OPP3 and OPP4. This work provides new insights into the structural flexibility and emission characteristics of OPP-TEA photoredox catalyst systems, potentially contributing to improved design strategies for organic chromophores in <math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mrow>\u0000 <mtext>CO</mtext>\u0000 </mrow>\u0000 <mrow>\u0000 <mn>2</mn>\u0000 </mrow>\u0000 </msub>\u0000 </mrow>\u0000 <annotation>$$ {mathrm{CO}}_2 $$</annotation>\u0000 </semantics></math> reduction applications.\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 4","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143083727","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Structural, Electronic and Vibrational Properties of LaCrO 3 $$ {}_3 $$ . A Quantum Mechanical Investigation by Using an All Electron Gaussian Type Basis Set and a Full Range Hybrid Functional

IF 3.4 3区化学

Journal of Computational Chemistry Pub Date : 2025-02-04 DOI: 10.1002/jcc.27523

Khaled E. El-Kelany, Alexander Platonenko, Klaus Doll, Roberto Dovesi

{"title":"The Structural, Electronic and Vibrational Properties of LaCrO\u0000 \u0000 \u0000 \u0000 \u0000 3\u0000 \u0000 \u0000 $$ {}_3 $$\u0000 . A Quantum Mechanical Investigation by Using an All Electron Gaussian Type Basis Set and a Full Range Hybrid Functional","authors":"Khaled E. El-Kelany, Alexander Platonenko, Klaus Doll, Roberto Dovesi","doi":"10.1002/jcc.27523","DOIUrl":"10.1002/jcc.27523","url":null,"abstract":"<div>\u0000 \u0000 The geometrical, electronic and vibrational properties of LaCrO<math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mrow></mrow>\u0000 <mn>3</mn>\u0000 </msub>\u0000 </mrow>\u0000 <annotation>$$ {}_3 $$</annotation>\u0000 </semantics></math> have been investigated by using an all electron Gaussian type basis set, the B3LYP functional and the CRYSTAL code, and compared with KVF<math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mrow></mrow>\u0000 <mn>3</mn>\u0000 </msub>\u0000 </mrow>\u0000 <annotation>$$ {}_3 $$</annotation>\u0000 </semantics></math>: in the two compounds the transition metal is formally in d<math>\u0000 <semantics>\u0000 <mrow>\u0000 <msup>\u0000 <mrow></mrow>\u0000 <mn>3</mn>\u0000 </msup>\u0000 </mrow>\u0000 <annotation>$$ {}^3 $$</annotation>\u0000 </semantics></math> configuration. The high spin t<math>\u0000 <semantics>\u0000 <mrow>\u0000 <msubsup>\u0000 <mrow></mrow>\u0000 <mrow>\u0000 <mn>2</mn>\u0000 <mi>g</mi>\u0000 </mrow>\u0000 <mn>3</mn>\u0000 </msubsup>\u0000 </mrow>\u0000 <annotation>$$ {}_{2g}^3 $$</annotation>\u0000 </semantics></math> ground state excludes the Jahn Teller deformation and the orbital ordering. The energy gain due to the rotation of the octahedra (from the cubic space group Pm<math>\u0000 <semantics>\u0000 <mrow>\u0000 <mover>\u0000 <mn>3</mn>\u0000 <mo>¯</mo>\u0000 </mover>\u0000 <mtext>m</mtext>\u0000 </mrow>\u0000 <annotation>$$ overline{3}mathrm{m} $$</annotation>\u0000 </semantics></math>, N. 221, to space group <math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>P</mi>\u0000 <mfrac>\u0000 <mn>4</mn>\u0000 <mi>m</mi>\u0000 </mfrac>\u0000 <mi>bm</mi>\u0000 </mrow>\u0000 <annotation>$$ Pfrac{4}{m} bm $$</annotation>\u0000 </semantics></math>, N.127, and to <math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>I</mi>\u0000 <mfrac>\u0000 <mn>4</mn>\u0000 <mi>m</mi>\u0000 </mfrac>\u0000 <mi>cm</mi>\u0000 </mrow>\u0000 <annotation>$$ Ifrac{4}{m} cm $$</annotation>\u0000 </semantics></math>, N. 140) in the oxide is about 70 times larger than in the fluoride (5.4 vs. 0.08 mE<math>\u0000 <semantics>\u0000 ","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 4","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143083917","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Rational Design for Antioxidant Diphenylamine Derivatives Using Quantitative Structure–Activity Relationships and Quantum Mechanics Calculations

IF 3.4 3区化学

Journal of Computational Chemistry Pub Date : 2025-02-03 DOI: 10.1002/jcc.70055

Ayokanmi Joseph Aremu, Phiphob Naweephattana, Ismail Dwi Putra, Borwornlak Toopradab, Phornphimon Maitarad, Thanyada Rungrotmongkol

{"title":"Rational Design for Antioxidant Diphenylamine Derivatives Using Quantitative Structure–Activity Relationships and Quantum Mechanics Calculations","authors":"Ayokanmi Joseph Aremu, Phiphob Naweephattana, Ismail Dwi Putra, Borwornlak Toopradab, Phornphimon Maitarad, Thanyada Rungrotmongkol","doi":"10.1002/jcc.70055","DOIUrl":"10.1002/jcc.70055","url":null,"abstract":"<div>\u0000 \u0000 Diphenylamine (DPA) derivatives, used as antioxidants in rubber-based products, inhibit autoxidation by donating hydrogen atoms to peroxyl radicals. Octanol–water partition coefficient (LogKow), an antioxidant index, helps predict their distribution in hydrophobic polymer matrices. Therefore, this study aimed to investigate the relationship between the structure of DPA derivatives and their antioxidant activities, using machine learning with quantitative structure–activity relationships (QSAR) and quantum mechanics (QM). The structure of DPA derivatives was optimized using Density Functional Theory and analyzed for molecular properties. The QSAR models were trained using important descriptors identified through permutation importance. Among the models developed, the Gradient Boosting Regressor (GBR) showed the best performance, with R2 of 0.983 and root mean square error (RMSE) of 0.642 for the test set. SHAP analysis revealed that molecular weight and electronic properties significantly influenced LogKow predictions. For instance, a higher molecular weight was associated with increased LogKow, and a higher positive charge of C2 correlated with higher LogKow predictions. Consequently, the two potent compounds (D1 and D2) were designed based on QSAR model guidance. The GBR model predicted LogKow values of 9.789 and 7.102 for D1 and D2, respectively, which are higher than the training compounds in the model. To gain molecular insight, the quantum chemical calculations with M062X/6–311++G(d,p)//M062X/6-31G(d,p) were performed to investigate the bond dissociation enthalpy (BDE). The results showed that D1 (79.50 kcal/mol) and D2 (72.43 kcal/mol) exhibited lower BDEs than the reference compounds, suggesting that the designed compounds have the potential for enhanced antioxidant activity. In addition, the antioxidant reaction mechanism was studied by using M062X/6–311++G(d,p)//M062X/6-31G(d,p) which found that the hydrogen atom transfer is the key step, where D1 and D2 showed activation energy barriers of 10.38 and 6.29 kcal/mol, respectively, compared to reference compounds of R3 (10.39 kcal/mol), R1 (10.40 kcal/mol), and R2 (18.26 kcal/mol). Therefore, our findings demonstrate that integrating QSAR with quantum chemical calculations can effectively guide the design of DPA derivatives with improved antioxidant properties.\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 4","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143083581","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Molecular and Electronic Structure and Properties of the Single Benzene-Based Fluorophores Containing Guanidine Subunit

IF 3.4 3区化学

Journal of Computational Chemistry Pub Date : 2025-02-03 DOI: 10.1002/jcc.70054

Zoran Glasovac, Davor Margetić, Ivana Antol

{"title":"Molecular and Electronic Structure and Properties of the Single Benzene-Based Fluorophores Containing Guanidine Subunit","authors":"Zoran Glasovac, Davor Margetić, Ivana Antol","doi":"10.1002/jcc.70054","DOIUrl":"10.1002/jcc.70054","url":null,"abstract":"The Gibbs energies of protonation (ΔGp) and the basic photophysical properties for single-benzene fluorophores (SBFs) containing guanidine and/or amino subunits and the changes that occur upon protonation were modeled by the TDDFT approach. The calculated ΔGp energies for amino SBFs in the S1 state range from 985 to 1100 kJ mol−1 which are below the values for guanidines. The protonation of the guanidine-SBFs induces a hypsochromic shift of the absorption and the emission maxima with the Stokes shift of > 100 nm in both cases. Isomerization through the ESIPT process is less probable than in amino-SBFs due to the unfavorable thermodynamics. Still, if it occurs, it leads to a strong red shift of the emission by > 150 nm. Aromaticity indices point to strong antiaromatic character of the examined guanidino-SBFs in the FC region which decreases upon geometrical relaxation and ESIPT. The excited state proton transfer occurs in guanidine-SBF/phenol complexes in the S1 state, stabilizing CT states and fluorescence quenching.","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 4","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70054","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143084175","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Probability Density Analysis Reveals Substantial Differences Between the Dinitrogen and Acetylene Triple Bonds

IF 3.4 3区化学

Journal of Computational Chemistry Pub Date : 2025-02-03 DOI: 10.1002/jcc.70037

Michel V. Heinz, Emma Gorgas, Nicole Maser, Arne Lüchow

{"title":"Probability Density Analysis Reveals Substantial Differences Between the Dinitrogen and Acetylene Triple Bonds","authors":"Michel V. Heinz, Emma Gorgas, Nicole Maser, Arne Lüchow","doi":"10.1002/jcc.70037","DOIUrl":"10.1002/jcc.70037","url":null,"abstract":"In earlier publications, it was shown that the electron positions maximizing the probability density <math>\u0000 <semantics>\u0000 <mrow>\u0000 <msup>\u0000 <mfenced>\u0000 <mi>Ψ</mi>\u0000 </mfenced>\u0000 <mn>2</mn>\u0000 </msup>\u0000 </mrow>\u0000 <annotation>$$ {left|Psi right|}^2 $$</annotation>\u0000 </semantics></math> resemble the Lewis structures for most small molecules. While this holds for the triple bond in acetylene, this is not the case for the triple bond in dinitrogen. Because of recent advances in studying the topology of wave functions, this peculiar case is revisited. In this work, the dinitrogen wave function is analyzed and compared to that of acetylene. Significant differences of the electron positions maximizing <math>\u0000 <semantics>\u0000 <mrow>\u0000 <msup>\u0000 <mfenced>\u0000 <mi>Ψ</mi>\u0000 </mfenced>\u0000 <mn>2</mn>\u0000 </msup>\u0000 </mrow>\u0000 <annotation>$$ {left|Psi right|}^2 $$</annotation>\u0000 </semantics></math> are uncovered and explained by the presence of hydrogen atoms in acetylene and by electron arrangements resulting from calculations of the nitrogen and carbon atoms. Moreover, insights into the electron delocalization of both molecules are gained by investigating electron exchange paths. Considering the different chemical behaviors of dinitrogen and acetylene, these differences should be expected.","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 4","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70037","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143084148","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Large-Scale FMO-MP2 Calculations of the Spike Protein Droplet Model

IF 3.4 3区化学

Journal of Computational Chemistry Pub Date : 2025-02-02 DOI: 10.1002/jcc.70052

Hideo Doi, Tatsuya Nakano, Kota Sakakura, Kazuki Akisawa, Koji Okuwaki, Yoshinori Hirano, Eiji Yamamoto, Kenji Yasuoka, Satoshi Ohshima, Takahiro Katagiri, Yuji Mochizuki

引用次数: 0

Projector-Based Quantum Embedding Study of Iron Complexes

IF 3.4 3区化学

Journal of Computational Chemistry Pub Date : 2025-01-29 DOI: 10.1002/jcc.70043

Jonathan M. Waldrop, Ajay Panyala, Daniel Mejia-Rodriguez, Theresa L. Windus, Niranjan Govind

{"title":"Projector-Based Quantum Embedding Study of Iron Complexes","authors":"Jonathan M. Waldrop, Ajay Panyala, Daniel Mejia-Rodriguez, Theresa L. Windus, Niranjan Govind","doi":"10.1002/jcc.70043","DOIUrl":"10.1002/jcc.70043","url":null,"abstract":"<div>\u0000 \u0000 Projection-based embedding theory (PBET) is used to calculate and assess the challenging spin-crossover energies for a selection of small Fe-containing systems by embedding the metal center into the frozen potential of the ligands. MP2, CCSD, and CCSD(T) are embedded in potentials from the SCAN and r2SCAN functionals and compared with the canonical values for the constituent methods and previously reported reference values. Considering the PBET calculations as a correction for the underlying DFT, the embedding calculations are able to provided improvement for most cases. In some cases, the PBET methods are able to compensate for limitations in the wave function methods and produce results similar to more rigorous calculations from the literature. For the systems with spin-crossover energies near zero, the current methodology fails to provide consistent improvement. The isolated recalculation of the electronic structure around the metal center when embedded into a DFT treatment of the ligand field shows promise as a pragmatic and lower cost treatment compared to the canonical treatment of the whole system of the difficult class of spin-crossover complexes.\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 3","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143056387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

PSSKB: A Web Application to Study Protein Structures PSSKB：研究蛋白质结构的网络应用程序

IF 3.4 3区化学

Journal of Computational Chemistry Pub Date : 2025-01-28 DOI: 10.1002/jcc.70046

Denis V. Petrovskiy, Kirill S. Nikolsky, Liudmila I. Kulikova, Vladimir R. Rudnev, Tatiana V. Butkova, Kristina A. Malsagova, Valeriya I. Nakhod, Arthur T. Kopylov, Anna L. Kaysheva

{"title":"PSSKB: A Web Application to Study Protein Structures","authors":"Denis V. Petrovskiy, Kirill S. Nikolsky, Liudmila I. Kulikova, Vladimir R. Rudnev, Tatiana V. Butkova, Kristina A. Malsagova, Valeriya I. Nakhod, Arthur T. Kopylov, Anna L. Kaysheva","doi":"10.1002/jcc.70046","DOIUrl":"10.1002/jcc.70046","url":null,"abstract":"<div>\u0000 \u0000 The proteins expressed during the cell cycle determine cell function and ensure signaling pathway activation in response to environmental influences. Developments in structural biology, biophysics, and bioinformatics provide information on the structure and function of particular proteins including that on the structural changes in proteins due to post-translational modification (PTM) and amino acid substitutions (AAS), which is essential for understanding protein function and life cycle. These are PTMs and AASs that often modulate the function and alter the stability and localization of a protein in a cell. PSSKB is a platform that integrates all necessary tools for modeling the five common natural modifications and all canonical AASs in proteins. The available tools are not limited to the local database, so the user can select a protein from Uniprot ID or PDB ID. The result will be a three-dimensional (3D) representation of the modified structure, as well as an analysis of the changes in the performance of the intact and modified structures after energy minimization compared with the original structure, which not only makes it possible to evaluate AAS/PTM influence of on a protein's characteristics but also to use the 3D model for further studies. Additionally, PSSKB enables the user to search, align, overlay, and determine the exact coordinates of protein structure fragments. The search results are a set of structural motifs similar to the query and ranked by statistical significance. The platform is fully functional and publicly available at https://psskb.org/. No registration is required to access the platform. A tutorial video can be found at https://psskb.org/page/about. Services provided on the platform are based on previously developed and published software. SCPacker applied for PTM Modeling and AAS services available at GitHub (https://github.com/protdb/SCPacker). SaFoldNet applied for a Similar Search service is also available at GitHub (https://github.com/protdb/ABBNet).\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 3","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143055437","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0