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Journal of Computer-aided Molecular Design

The Journal of Computer-Aided Molecular Design is a leading scientific journal that focuses on the application of computational methods and techniques in the field of molecular design. It publishes cutting-edge research articles, reviews, and perspectives that explore the use of computer-aided tools for drug discovery, molecular modeling, virtual screening, and structure-based design. This interdisciplinary journal serves as a platform for researchers and practitioners to share advancements in computational chemistry and molecular biology, fostering innovation and collaboration in the field.
Details
Abbr. J Comput Aided Mol Des
Publisher Springer
Start 1987
End Continuing
Frequency Monthly, <2002->
p-ISSN 0920-654X
e-ISSN 1573-4951
Country Netherlands
Language English
Specialties Molecular Biology
Biomedical Engineering
Metrics
h-index / Ranks: 2271 119
SJR / Ranks: 7389 609
CiteScore / Ranks: 2600 7.40
JIF / Ranks: 2766 3.5
Recent Articles
11.
Promoter recognition specificity of Corynebacterium glutamicum stress response sigma factors σ and σ deciphered using computer modeling and point mutagenesis
Blumenstein J, Dostalova H, Rucka L, Stepanek V, Busche T, Kalinowski J, et al.
J Comput Aided Mol Des . 2024 Nov; 39(1):1. PMID: 39585436
This study aimed to reveal interactions of the stress response sigma subunits (factors) σ and σ of RNA polymerase and promoters in Gram-positive bacterium Corynebacterium glutamicum by combining wet-lab obtained...
12.
Understanding the relationship between preferential interactions of peptides in water-acetonitrile mixtures with protein-solvent contact surface area
Phougat M, Sahni N, Choudhury D
J Comput Aided Mol Des . 2024 Nov; 38(1):38. PMID: 39537830
The influence of polar, water-miscible organic solvents (POS) on protein structure, stability, and functional activity is a subject of significant interest and complexity. This study examines the effects of acetonitrile...
13.
Identification of novel inhibitors targeting PI3Kα via ensemble-based virtual screening method, biological evaluation and molecular dynamics simulation
Zhang H, Qi H, Li Y, Shi X, Hu M, Chen X, et al.
J Comput Aided Mol Des . 2024 Nov; 38(1):37. PMID: 39528618
PIK3CA gene encoding PI3K p110α is one of the most frequently mutated and overexpressed in majority of human cancers. Development of potent and selective novel inhibitors targeting PI3Kα was considered...
14.
Computational Identification and Illustrative Standard for Representation of Unimolecular G-Quadruplex Secondary Structures (CIIS-GQ)
Direk T, Doluca O
J Comput Aided Mol Des . 2024 Oct; 38(1):35. PMID: 39470927
G-quadruplexes refer to a large group of nucleic acid-based structures. In recent years, they have been attracting attention due to their biological roles in the telomeres and promoter regions. These...
15.
Comparative assessment of physics-based in silico methods to calculate relative solubilities
Garaizar Suarez A, Goller A, Beck M, Gheta S, Meier K
J Comput Aided Mol Des . 2024 Oct; 38(1):36. PMID: 39470860
Relative solubilities, i.e. whether a given molecule is more soluble in one solvent compared to others, is a critical parameter for pharmaceutical and agricultural formulation development and chemical synthesis, material...
16.
Steered molecular dynamics simulation as a post-process to optimize the iBRAB-designed Fab model
Do P, Le V
J Comput Aided Mol Des . 2024 Oct; 38(1):34. PMID: 39443337
Therapeutic monoclonal antibodies are an effective method of treating acute infectious diseases. However, knowing which of the produced antibodies in the vast number of human antibodies can cure the disease...
17.
Structure-based pose prediction: Non-cognate docking extended to macrocyclic ligands
Cleves A, Tandon H, Jain A
J Comput Aided Mol Des . 2024 Oct; 38(1):33. PMID: 39414633
So-called "cross-docking" is the prediction of the bound configuration of small-molecule ligands that differ from the cognate ligand of a protein co-crystal structure. This is a much more challenging problem...
18.
De novo drug design through gradient-based regularized search in information-theoretically controlled latent space
Jang H, Seo S, Park S, Kim B, Choi G, Choi J, et al.
J Comput Aided Mol Des . 2024 Aug; 38(1):32. PMID: 39190191
Over the last decade, automatic chemical design frameworks for discovering molecules with drug-like properties have significantly progressed. Among them, the variational autoencoder (VAE) is a cutting-edge approach that models the...
19.
Computational design and experimental confirmation of a disulfide-stapled YAP helix-trap derived from TEAD4 helical hairpin to selectively capture YAP α1-helix with potent antitumor activity
Li K, Liu L
J Comput Aided Mol Des . 2024 Aug; 38(1):31. PMID: 39177727
Human Hippo signaling pathway is an evolutionarily conserved regulator network that controls organ development and has been implicated in various cancers. Transcriptional enhanced associate domain-4 (TEAD4) is the final nuclear...
20.
Holistic in silico developability assessment of novel classes of small proteins using publicly available sequence-based predictors
Pais D, Mayer J, Felderer K, Batalha M, Eichner T, Santos S, et al.
J Comput Aided Mol Des . 2024 Aug; 38(1):30. PMID: 39164492
The development of novel therapeutic proteins is a lengthy and costly process, with an average attrition rate of 91% (Thomas et al. Clinical Development Success Rates and Contributing Factors 2011-2020,...