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Most Monogenic Disorders Are Caused by Mutations Altering Protein Folding Free Energy.
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- International Journal of Molecular Sciences, 2024, v. 25, n. 4, p. 1963, doi. 10.3390/ijms25041963
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- Article
Predicting the Effect of Single Mutations on Protein Stability and Binding with Respect to Types of Mutations.
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- International Journal of Molecular Sciences, 2023, v. 24, n. 15, p. 12073, doi. 10.3390/ijms241512073
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- Article
PKAD-2: New Entries and Expansion of Functionalities of the Database of Experimentally Measured pKa's of Proteins.
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- Journal of Computational Biophysics & Chemistry, 2023, v. 22, n. 5, p. 515, doi. 10.1142/S2737416523500230
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- Article
Electrostatics in Computational Biophysics and Its Implications for Disease Effects.
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- International Journal of Molecular Sciences, 2022, v. 23, n. 18, p. N.PAG, doi. 10.3390/ijms231810347
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- Article
SAMPDI-3D: predicting the effects of protein and DNA mutations on protein–DNA interactions.
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- Bioinformatics, 2021, v. 37, n. 21, p. 3760, doi. 10.1093/bioinformatics/btab567
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- Article
Opioid Addiction and Opioid Receptor Dimerization: Structural Modeling of the OPRD1 and OPRM1 Heterodimer and Its Signaling Pathways.
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- International Journal of Molecular Sciences, 2021, v. 22, n. 19, p. 10290, doi. 10.3390/ijms221910290
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- Article
Computational Investigation of the pH Dependence of Stability of Melanosome Proteins: Implication for Melanosome formation and Disease.
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- International Journal of Molecular Sciences, 2021, v. 22, n. 15, p. 8273, doi. 10.3390/ijms22158273
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- Article
Making Sense of Genetic Information: The Promising Evolution of Clinical Stratification and Precision Oncology Using Machine Learning.
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- Genes, 2021, v. 12, n. 5, p. 722, doi. 10.3390/genes12050722
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- Article
In Silico Analysis of the Molecular-Level Impact of SMPD1 Variants on Niemann-Pick Disease Severity.
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- International Journal of Molecular Sciences, 2021, v. 22, n. 9, p. 4516, doi. 10.3390/ijms22094516
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- Article
SAAMBE-SEQ: a sequence-based method for predicting mutation effect on protein–protein binding affinity.
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- Bioinformatics, 2021, v. 37, n. 7, p. 992, doi. 10.1093/bioinformatics/btaa761
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- Article
Editorial: Special Issue on Computational Chemistry Methods to Predict pKa's of Ionizable Groups in Proteins, RNAs, DNAs and Small Molecules.
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- 2021
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- Editorial
pH-Dependent Interactions of Apolipophorin-III with a Lipid Disk.
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- Journal of Computational Biophysics & Chemistry, 2021, v. 20, n. 2, p. 153, doi. 10.1142/S2737416520420041
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- Article
On regularization of charge singularities in solving the Poisson-Boltzmann equation with a smooth solute-solvent boundary.
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- Mathematical Biosciences & Engineering, 2021, v. 18, n. 2, p. 1370, doi. 10.3934/mbe.2021072
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- Article
Towards More Biology-Oriented Papers: Name Change of the Journal of Theoretical and Computational Chemistry to Journal of Computational Biophysics and Chemistry.
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- 2021
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- Publication type:
- Editorial
SAAFEC-SEQ: A Sequence-Based Method for Predicting the Effect of Single Point Mutations on Protein Thermodynamic Stability.
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- International Journal of Molecular Sciences, 2021, v. 22, n. 2, p. 606, doi. 10.3390/ijms22020606
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- Article
BION-2: Predicting Positions of Non-Specifically Bound Ions on Protein Surface by a Gaussian-Based Treatment of Electrostatics.
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- International Journal of Molecular Sciences, 2021, v. 22, n. 1, p. 272, doi. 10.3390/ijms22010272
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- Article
Strain-induced packing transition of Ih Cu<sub>n</sub>@Ag<sub>55-n</sub>(n=0, 1, 13, 43) clusters from atomic simulations.
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- Mathematical Biosciences & Engineering, 2020, v. 17, n. 6, p. 6390, doi. 10.3934/mbe.2020336
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- Article
An Ensemble Approach to Predict the Pathogenicity of Synonymous Variants.
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- Genes, 2020, v. 11, n. 9, p. 1102, doi. 10.3390/genes11091102
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- Article
SAAMBE-3D: Predicting Effect of Mutations on Protein–Protein Interactions.
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- International Journal of Molecular Sciences, 2020, v. 21, n. 7, p. 2563, doi. 10.3390/ijms21072563
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- Article
Evaluation of performance of leading algorithms for variant pathogenicity predictions and designing a combinatory predictor method: application to Rett syndrome variants.
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- PeerJ, 2019, p. 1, doi. 10.7717/peerj.8106
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- Article
DelPhi Suite: New Developments and Review of Functionalities.
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- Journal of Computational Chemistry, 2019, v. 40, n. 28, p. 2502, doi. 10.1002/jcc.26006
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- Article
Novel Genetic Markers for Early Detection of Elevated Breast Cancer Risk in Women.
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- International Journal of Molecular Sciences, 2019, v. 20, n. 19, p. 4828, doi. 10.3390/ijms20194828
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- Article
A super-Gaussian Poisson–Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states.
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- Journal of Mathematical Biology, 2019, v. 79, n. 2, p. 631, doi. 10.1007/s00285-019-01372-1
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- Article
A grid‐based algorithm in conjunction with a gaussian‐based model of atoms for describing molecular geometry.
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- Journal of Computational Chemistry, 2019, v. 40, n. 12, p. 1290, doi. 10.1002/jcc.25786
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- Article
Processivity vs. Beating: Comparing Cytoplasmic and Axonemal Dynein Microtubule Binding Domain Association with Microtubule.
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- International Journal of Molecular Sciences, 2019, v. 20, n. 5, p. 1090, doi. 10.3390/ijms20051090
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- Article
Structural Perspective on Revealing and Altering Molecular Functions of Genetic Variants Linked with Diseases.
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- International Journal of Molecular Sciences, 2019, v. 20, n. 3, p. 548, doi. 10.3390/ijms20030548
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- Article
PKAD: a database of experimentally measured pKa values of ionizable groups in proteins.
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- Database: The Journal of Biological Databases & Curation, 2019, v. 2019, p. N.PAG, doi. 10.1093/database/baz024
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- Article
DelPhiPKa: Including salt in the calculations and enabling polar residues to titrate.
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- Proteins, 2018, v. 86, n. 12, p. 1277, doi. 10.1002/prot.25608
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- Article
E-hooks provide guidance and a soft landing for the microtubule binding domain of dynein.
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- Scientific Reports, 2018, v. 8, n. 1, p. 1, doi. 10.1038/s41598-018-31480-9
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- Article
Predicting protein--DNA binding free energy change upon missense mutations using modified MM/PBSA approach: SAMPDI webserver.
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- Bioinformatics, 2018, v. 34, n. 5, p. 779, doi. 10.1093/bioinformatics/btx698
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- Article
Computational Investigation of the Missense Mutations in DHCR7 Gene Associated with Smith-Lemli-Opitz Syndrome.
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- International Journal of Molecular Sciences, 2018, v. 19, n. 1, p. 141, doi. 10.3390/ijms19010141
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- Article
DelPhiForce web server: electrostatic forces and energy calculations and visualization.
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- Bioinformatics, 2017, v. 33, n. 22, p. 3661, doi. 10.1093/bioinformatics/btx495
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- Article
Treating ion distribution with Gaussian-based smooth dielectric function in DelPhi.
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- Journal of Computational Chemistry, 2017, v. 38, n. 22, p. 1974, doi. 10.1002/jcc.24831
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- Article
DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding.
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- Journal of Computational Chemistry, 2017, v. 38, n. 9, p. 584, doi. 10.1002/jcc.24715
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- Article
Computational investigation of proton transfer, p Ka shifts and p H-optimum of protein- DNA and protein- RNA complexes.
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- Proteins, 2017, v. 85, n. 2, p. 282, doi. 10.1002/prot.25221
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- Article
Cofactors-loaded quaternary structure of lysine-specific demethylase 5C (KDM5C) protein: Computational model.
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- Proteins, 2016, v. 84, n. 12, p. 1797, doi. 10.1002/prot.25162
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- Article
Electrostatic component of binding energy: Interpreting predictions from poisson-boltzmann equation and modeling protocols.
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- Journal of Computational Chemistry, 2016, v. 37, n. 28, p. 2495, doi. 10.1002/jcc.24475
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- Article
Cytoplasmic dynein binding, run length, and velocity are guided by long-range electrostatic interactions.
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- Scientific Reports, 2016, p. 31523, doi. 10.1038/srep31523
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- Publication type:
- Article
SAAFEC: Predicting the Effect of Single Point Mutations on Protein Folding Free Energy Using a Knowledge-Modified MM/PBSA Approach.
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- International Journal of Molecular Sciences, 2016, v. 17, n. 4, p. 512, doi. 10.3390/ijms17040512
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- Article
SAAMBE:Webserver to Predict the Charge of Binding Free Energy Caused by Amino Acids Mutations.
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- International Journal of Molecular Sciences, 2016, v. 17, n. 4, p. 547, doi. 10.3390/ijms17040547
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- Article
Multiscale method for modeling binding phenomena involving large objects: application to kinesin motor domains motion along microtubules.
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- Scientific Reports, 2016, p. 23249, doi. 10.1038/srep23249
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- Article
DelPhiPKa web server: predicting pK<sub>a</sub> of proteins, RNAs and DNAs.
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- Bioinformatics, 2016, v. 32, n. 4, p. 614, doi. 10.1093/bioinformatics/btv607
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- Article
Investigating the linkage between disease-causing amino acid variants and their effect on protein stability and binding.
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- Proteins, 2016, v. 84, n. 2, p. 232, doi. 10.1002/prot.24968
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- Article
Revealing the Effects of Missense Mutations Causing Snyder-Robinson Syndrome on the Stability and Dimerization of Spermine Synthase.
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- International Journal of Molecular Sciences, 2016, v. 17, n. 1, p. 77, doi. 10.3390/ijms17010077
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- Article
Statistical Investigation of Surface Bound Ions and Further Development of BION Server to Include pH and Salt Dependence.
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- Journal of Computational Chemistry, 2015, v. 36, n. 32, p. 2381, doi. 10.1002/jcc.24218
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- Article
pKa predictions for proteins, RNAs, and DNAs with the Gaussian dielectric function using DelPhi pKa.
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- Proteins, 2015, v. 83, n. 12, p. 2186, doi. 10.1002/prot.24935
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- Article
Mutations in the KDM5C ARID Domain and Their Plausible Association with Syndromic Claes-Jensen-Type Disease.
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- International Journal of Molecular Sciences, 2015, v. 16, n. 11, p. 22270, doi. 10.3390/ijms161126022
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- Article
ZC4H2, an XLID gene, is required for the generation of a specific subset of CNS interneurons.
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- Human Molecular Genetics, 2015, v. 24, n. 17, p. 4848, doi. 10.1093/hmg/ddv208
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- Article
Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method.
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- PLoS Computational Biology, 2015, v. 11, n. 7, p. 1, doi. 10.1371/journal.pcbi.1004276
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- Article
On Human Disease-Causing Amino Acid Variants: Statistical Study of Sequence and Structural Patterns.
- Published in:
- Human Mutation, 2015, v. 36, n. 5, p. 524, doi. 10.1002/humu.22770
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- Article