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For: Li M, Petukh M, Alexov E, Panchenko AR. Predicting the Impact of Missense Mutations on Protein-Protein Binding Affinity. J Chem Theory Comput 2014;10:1770-1780. [PMID: 24803870 PMCID: PMC3985714 DOI: 10.1021/ct401022c] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Indexed: 01/22/2023]
Number Cited by Other Article(s)
1
Fu H, Mo X, Ivanov AA. Decoding the functional impact of the cancer genome through protein-protein interactions. Nat Rev Cancer 2025;25:189-208. [PMID: 39810024 DOI: 10.1038/s41568-024-00784-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/02/2024] [Indexed: 01/16/2025]
2
Zheng F, Jiang X, Wen Y, Yang Y, Li M. Systematic investigation of machine learning on limited data: A study on predicting protein-protein binding strength. Comput Struct Biotechnol J 2024;23:460-472. [PMID: 38235359 PMCID: PMC10792694 DOI: 10.1016/j.csbj.2023.12.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/14/2023] [Accepted: 12/16/2023] [Indexed: 01/19/2024]  Open
3
Budi T, Kumnan N, Singchat W, Chalermwong P, Thong T, Wongloet W, Faniriharisoa Maxime Toky R, Pathomvanich P, Panthum T, Wattanadilokchatkun P, Farhan Ahmad S, Tanglertpaibul N, Vangnai K, Chaiyes A, Yokthongwattana C, Sinthuvanich C, Han K, Muangmai N, Koga A, Nunome M, Sawatdichaikul O, Duengkae P, Matsuda Y, Srikulnath K. Weak purifying selection in allelic diversity of the ADSL gene in indigenous and local chicken breeds and red junglefowl in Thailand. Gene 2024;923:148587. [PMID: 38768877 DOI: 10.1016/j.gene.2024.148587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 05/01/2024] [Accepted: 05/16/2024] [Indexed: 05/22/2024]
4
Ridha F, Gromiha MM. MPA-MutPred: a novel strategy for accurately predicting the binding affinity change upon mutation in membrane protein complexes. Brief Bioinform 2024;25:bbae598. [PMID: 39550225 PMCID: PMC11568875 DOI: 10.1093/bib/bbae598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 10/10/2024] [Accepted: 11/04/2024] [Indexed: 11/18/2024]  Open
5
Mechidi P, Holien J, Grando D, Huynh T, Lawrie AC. New Sources of Resistance to Terbinafine Revealed and Squalene Epoxidase Modelled in the Dermatophyte Fungus Trichophyton interdigitale From Australia. Mycoses 2024;67:e13795. [PMID: 39304967 DOI: 10.1111/myc.13795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Accepted: 08/21/2024] [Indexed: 09/22/2024]
6
Guclu TF, Atilgan AR, Atilgan C. Deciphering GB1's Single Mutational Landscape: Insights from MuMi Analysis. J Phys Chem B 2024;128:7987-7996. [PMID: 39115184 PMCID: PMC11671028 DOI: 10.1021/acs.jpcb.4c04916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 08/02/2024] [Accepted: 08/02/2024] [Indexed: 08/23/2024]
7
Tripathi V, Khare A, Shukla D, Bharadwaj S, Kirtipal N, Ranjan V. Genomic and computational-aided integrative drug repositioning strategy for EGFR and ROS1 mutated NSCLC. Int Immunopharmacol 2024;139:112682. [PMID: 39029228 DOI: 10.1016/j.intimp.2024.112682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 07/02/2024] [Accepted: 07/11/2024] [Indexed: 07/21/2024]
8
Gurusinghe SNS, Wu Y, DeGrado W, Shifman JM. ProBASS - a language model with sequence and structural features for predicting the effect of mutations on binding affinity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.21.600041. [PMID: 38979193 PMCID: PMC11230163 DOI: 10.1101/2024.06.21.600041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
9
Nandigrami P, Fiser A. Assessing the functional impact of protein binding site definition. Protein Sci 2024;33:e5026. [PMID: 38757384 PMCID: PMC11099757 DOI: 10.1002/pro.5026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 05/01/2024] [Accepted: 05/03/2024] [Indexed: 05/18/2024]
10
Hussin A, Nathan S, Shahidan MA, Nor Rahim MY, Zainun MY, Khairuddin NAN, Ibrahim N. Identification and mechanism determination of the efflux pump subunit amrB gene mutations linked to gentamicin susceptibility in clinical Burkholderia pseudomallei from Malaysian Borneo. Mol Genet Genomics 2024;299:12. [PMID: 38381232 DOI: 10.1007/s00438-024-02105-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 12/29/2023] [Indexed: 02/22/2024]
11
Mills KR, Torabifard H. Computational approaches to investigate fluoride binding, selectivity and transport across the membrane. Methods Enzymol 2024;696:109-154. [PMID: 38658077 DOI: 10.1016/bs.mie.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
12
Rana MM, Nguyen DD. Geometric Graph Learning to Predict Changes in Binding Free Energy and Protein Thermodynamic Stability upon Mutation. J Phys Chem Lett 2023;14:10870-10879. [PMID: 38032742 DOI: 10.1021/acs.jpclett.3c02679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
13
Islam S, Pantazes RJ. Developing similarity matrices for antibody-protein binding interactions. PLoS One 2023;18:e0293606. [PMID: 37883504 PMCID: PMC10602319 DOI: 10.1371/journal.pone.0293606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/17/2023] [Indexed: 10/28/2023]  Open
14
Shirvanizadeh N, Vihinen M. VariBench, new variation benchmark categories and data sets. FRONTIERS IN BIOINFORMATICS 2023;3:1248732. [PMID: 37795169 PMCID: PMC10546188 DOI: 10.3389/fbinf.2023.1248732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 09/08/2023] [Indexed: 10/06/2023]  Open
15
Yang Z, Ye Z, Qiu J, Feng R, Li D, Hsieh C, Allcock J, Zhang S. A mutation-induced drug resistance database (MdrDB). Commun Chem 2023;6:123. [PMID: 37316673 DOI: 10.1038/s42004-023-00920-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 06/02/2023] [Indexed: 06/16/2023]  Open
16
PSnpBind-ML: predicting the effect of binding site mutations on protein-ligand binding affinity. J Cheminform 2023;15:31. [PMID: 36864534 PMCID: PMC9983232 DOI: 10.1186/s13321-023-00701-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/17/2023] [Indexed: 03/04/2023]  Open
17
Nandigrami P, Fiser A. Assessing the functional impact of protein binding site definition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525812. [PMID: 36747792 PMCID: PMC9900911 DOI: 10.1101/2023.01.26.525812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
18
Identification of NRAS Diagnostic Biomarkers and Drug Targets for Endometrial Cancer-An Integrated in Silico Approach. Int J Mol Sci 2022;23:ijms232214285. [PMID: 36430761 PMCID: PMC9692821 DOI: 10.3390/ijms232214285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/19/2022]  Open
19
Yu Y, Wang Z, Wang L, Tian S, Hou T, Sun H. Predicting the mutation effects of protein–ligand interactions via end-point binding free energy calculations: strategies and analyses. J Cheminform 2022;14:56. [PMID: 35987841 PMCID: PMC9392442 DOI: 10.1186/s13321-022-00639-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 08/08/2022] [Indexed: 12/04/2022]  Open
20
On the Rapid Calculation of Binding Affinities for Antigen and Antibody Design and Affinity Maturation Simulations. Antibodies (Basel) 2022;11:antib11030051. [PMID: 35997345 PMCID: PMC9397028 DOI: 10.3390/antib11030051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/23/2022] [Accepted: 08/01/2022] [Indexed: 02/05/2023]  Open
21
Li Y, Zhang R, Wang C, Forouhar F, Clarke OB, Vorobiev S, Singh S, Montelione GT, Szyperski T, Xu Y, Hunt JF. Oligomeric interactions maintain active-site structure in a noncooperative enzyme family. EMBO J 2022;41:e108368. [PMID: 35801308 DOI: 10.15252/embj.2021108368] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 04/07/2022] [Accepted: 04/16/2022] [Indexed: 11/09/2022]  Open
22
Pabbathi A, Coleman L, Godar S, Paul A, Garlapati A, Spencer M, Eller J, Alper JD. Long-range electrostatic interactions significantly modulate the affinity of dynein for microtubules. Biophys J 2022;121:1715-1726. [PMID: 35346642 PMCID: PMC9117880 DOI: 10.1016/j.bpj.2022.03.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/13/2022] [Accepted: 03/24/2022] [Indexed: 11/02/2022]  Open
23
Koshlan T, Kulikov K. Analysis to determine the effect of mutations on binding to small chemical molecules. J Bioinform Comput Biol 2022;20:2240003. [DOI: 10.1142/s0219720022400030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
24
Lai J, Yang J, Gamsiz Uzun ED, Rubenstein BM, Sarkar IN. LYRUS: a machine learning model for predicting the pathogenicity of missense variants. BIOINFORMATICS ADVANCES 2021;2:vbab045. [PMID: 35036922 PMCID: PMC8754197 DOI: 10.1093/bioadv/vbab045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 12/08/2021] [Accepted: 12/21/2021] [Indexed: 01/27/2023]
25
Sun T, Chen Y, Wen Y, Zhu Z, Li M. PremPLI: a machine learning model for predicting the effects of missense mutations on protein-ligand interactions. Commun Biol 2021;4:1311. [PMID: 34799678 PMCID: PMC8604987 DOI: 10.1038/s42003-021-02826-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 10/26/2021] [Indexed: 02/07/2023]  Open
26
Li G, Pahari S, Murthy AK, Liang S, Fragoza R, Yu H, Alexov E. SAAMBE-SEQ: a sequence-based method for predicting mutation effect on protein-protein binding affinity. Bioinformatics 2021;37:992-999. [PMID: 32866236 PMCID: PMC8128451 DOI: 10.1093/bioinformatics/btaa761] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 08/17/2020] [Accepted: 08/24/2020] [Indexed: 01/04/2023]  Open
27
Patel D, Patel JS, Ytreberg FM. Implementing and Assessing an Alchemical Method for Calculating Protein-Protein Binding Free Energy. J Chem Theory Comput 2021;17:2457-2464. [PMID: 33709712 PMCID: PMC8044032 DOI: 10.1021/acs.jctc.0c01045] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
28
Ochoa R, Laskowski RA, Thornton JM, Cossio P. Impact of Structural Observables From Simulations to Predict the Effect of Single-Point Mutations in MHC Class II Peptide Binders. Front Mol Biosci 2021;8:636562. [PMID: 34222328 PMCID: PMC8253603 DOI: 10.3389/fmolb.2021.636562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/15/2021] [Indexed: 11/23/2022]  Open
29
Chen Y, Lu H, Zhang N, Zhu Z, Wang S, Li M. PremPS: Predicting the impact of missense mutations on protein stability. PLoS Comput Biol 2020;16:e1008543. [PMID: 33378330 PMCID: PMC7802934 DOI: 10.1371/journal.pcbi.1008543] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 01/12/2021] [Accepted: 11/16/2020] [Indexed: 12/12/2022]  Open
30
Huang X, Zheng W, Pearce R, Zhang Y. SSIPe: accurately estimating protein-protein binding affinity change upon mutations using evolutionary profiles in combination with an optimized physical energy function. Bioinformatics 2020;36:2429-2437. [PMID: 31830252 DOI: 10.1093/bioinformatics/btz926] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 11/08/2019] [Accepted: 12/09/2019] [Indexed: 11/13/2022]  Open
31
Meseguer A, Dominguez L, Bota PM, Aguirre‐Plans J, Bonet J, Fernandez‐Fuentes N, Oliva B. Using collections of structural models to predict changes of binding affinity caused by mutations in protein-protein interactions. Protein Sci 2020;29:2112-2130. [PMID: 32797645 PMCID: PMC7513729 DOI: 10.1002/pro.3930] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 12/24/2022]
32
Zhang N, Lu H, Chen Y, Zhu Z, Yang Q, Wang S, Li M. PremPRI: Predicting the Effects of Missense Mutations on Protein-RNA Interactions. Int J Mol Sci 2020;21:ijms21155560. [PMID: 32756481 PMCID: PMC7432928 DOI: 10.3390/ijms21155560] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/28/2020] [Accepted: 07/30/2020] [Indexed: 12/23/2022]  Open
33
Shringari SR, Giannakoulias S, Ferrie JJ, Petersson EJ. Rosetta custom score functions accurately predict ΔΔG of mutations at protein-protein interfaces using machine learning. Chem Commun (Camb) 2020;56:6774-6777. [PMID: 32441721 DOI: 10.1039/d0cc01959c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
34
Pahari S, Li G, Murthy AK, Liang S, Fragoza R, Yu H, Alexov E. SAAMBE-3D: Predicting Effect of Mutations on Protein-Protein Interactions. Int J Mol Sci 2020;21:E2563. [PMID: 32272725 PMCID: PMC7177817 DOI: 10.3390/ijms21072563] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/04/2020] [Accepted: 04/05/2020] [Indexed: 12/26/2022]  Open
35
Zhang N, Chen Y, Lu H, Zhao F, Alvarez RV, Goncearenco A, Panchenko AR, Li M. MutaBind2: Predicting the Impacts of Single and Multiple Mutations on Protein-Protein Interactions. iScience 2020;23:100939. [PMID: 32169820 PMCID: PMC7068639 DOI: 10.1016/j.isci.2020.100939] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 11/21/2019] [Accepted: 02/20/2020] [Indexed: 01/17/2023]  Open
36
Ahmed Awan Z, Bima A, Rashidi OM, Jamil K, Khan IA, Almukadi HS, Bilgrami AL, Ahmad Shaik N, Banaganapalli B. Low resolution protein mapping and KB-R7943 drug-protein molecular interaction analysis of long-QT syndrome linked KCNH2 mutations. ALL LIFE 2020. [DOI: 10.1080/26895293.2020.1737249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]  Open
37
Wang E, Sun H, Wang J, Wang Z, Liu H, Zhang JZH, Hou T. End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design. Chem Rev 2019;119:9478-9508. [DOI: 10.1021/acs.chemrev.9b00055] [Citation(s) in RCA: 578] [Impact Index Per Article: 96.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
38
Junaid M, Li CD, Shah M, Khan A, Guo H, Wei DQ. Extraction of molecular features for the drug discovery targeting protein-protein interaction of Helicobacter pylori CagA and tumor suppressor protein ASSP2. Proteins 2019;87:837-849. [PMID: 31134671 DOI: 10.1002/prot.25748] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 05/04/2019] [Accepted: 05/22/2019] [Indexed: 12/13/2022]
39
Clark AJ, Negron C, Hauser K, Sun M, Wang L, Abel R, Friesner RA. Relative Binding Affinity Prediction of Charge-Changing Sequence Mutations with FEP in Protein-Protein Interfaces. J Mol Biol 2019;431:1481-1493. [PMID: 30776430 PMCID: PMC6453258 DOI: 10.1016/j.jmb.2019.02.003] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 01/17/2019] [Accepted: 02/04/2019] [Indexed: 01/16/2023]
40
Peng Y, Alexov E, Basu S. Structural Perspective on Revealing and Altering Molecular Functions of Genetic Variants Linked with Diseases. Int J Mol Sci 2019;20:ijms20030548. [PMID: 30696058 PMCID: PMC6386852 DOI: 10.3390/ijms20030548] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 01/25/2019] [Accepted: 01/26/2019] [Indexed: 12/25/2022]  Open
41
Geng C, Xue LC, Roel‐Touris J, Bonvin AMJJ. Finding the ΔΔ G spot: Are predictors of binding affinity changes upon mutations in protein–protein interactions ready for it? WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2019. [DOI: 10.1002/wcms.1410] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
42
Maheepala DC, Emerling CA, Rajewski A, Macon J, Strahl M, Pabón-Mora N, Litt A. Evolution and Diversification of FRUITFULL Genes in Solanaceae. FRONTIERS IN PLANT SCIENCE 2019;10:43. [PMID: 30846991 PMCID: PMC6394111 DOI: 10.3389/fpls.2019.00043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 01/11/2019] [Indexed: 05/12/2023]
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PremPDI estimates and interprets the effects of missense mutations on protein-DNA interactions. PLoS Comput Biol 2018;14:e1006615. [PMID: 30533007 PMCID: PMC6303081 DOI: 10.1371/journal.pcbi.1006615] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 12/21/2018] [Accepted: 11/01/2018] [Indexed: 01/01/2023]  Open
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Geng C, Vangone A, Folkers GE, Xue LC, Bonvin AMJJ. iSEE: Interface structure, evolution, and energy-based machine learning predictor of binding affinity changes upon mutations. Proteins 2018;87:110-119. [PMID: 30417935 PMCID: PMC6587874 DOI: 10.1002/prot.25630] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 10/19/2018] [Accepted: 11/05/2018] [Indexed: 02/06/2023]
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Dobson L, Mészáros B, Tusnády GE. Structural Principles Governing Disease-Causing Germline Mutations. J Mol Biol 2018;430:4955-4970. [DOI: 10.1016/j.jmb.2018.10.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 10/11/2018] [Indexed: 01/03/2023]
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Liu Q, Chen P, Wang B, Zhang J, Li J. dbMPIKT: a database of kinetic and thermodynamic mutant protein interactions. BMC Bioinformatics 2018;19:455. [PMID: 30482172 PMCID: PMC6260753 DOI: 10.1186/s12859-018-2493-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 11/13/2018] [Indexed: 02/06/2023]  Open
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Šoštarić N, O'Reilly FJ, Giansanti P, Heck AJR, Gavin AC, van Noort V. Effects of Acetylation and Phosphorylation on Subunit Interactions in Three Large Eukaryotic Complexes. Mol Cell Proteomics 2018;17:2387-2401. [PMID: 30181345 DOI: 10.1074/mcp.ra118.000892] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/27/2018] [Indexed: 01/18/2023]  Open
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Computational Approaches to Prioritize Cancer Driver Missense Mutations. Int J Mol Sci 2018;19:ijms19072113. [PMID: 30037003 PMCID: PMC6073793 DOI: 10.3390/ijms19072113] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 07/02/2018] [Accepted: 07/05/2018] [Indexed: 12/31/2022]  Open
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Jia Z, Li L, Peng Y, Ding F, Alexov E. The capricious electrostatic force: Revealing the signaling pathway in integrin α2-I domain. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2018. [DOI: 10.1142/s0219633618400011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Barlow KA, Ó Conchúir S, Thompson S, Suresh P, Lucas JE, Heinonen M, Kortemme T. Flex ddG: Rosetta Ensemble-Based Estimation of Changes in Protein-Protein Binding Affinity upon Mutation. J Phys Chem B 2018;122:5389-5399. [PMID: 29401388 DOI: 10.1021/acs.jpcb.7b11367] [Citation(s) in RCA: 163] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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